The Doctor and the Pegasus
by RandomHamster33
Summary: (Based somewhat off "Doctor Whooves and the Assistant") The Doctor finds himself in-guess where-Ponyville! Well, seems he hit somepony out of the sky. Too bad. But what's lurking in the dark, preparing to strike? Who will go missing, and who will leave? Find out.
1. Why am I Here

"Oi! Where in the solar system is that sonic screw driver?" the Doctor shouted to himself, trying to locate the handy little probe and control the TARDIS at the same time. She was going crazy, sparks flying up from the circuits and tumbling through time like a penny in a washing machine. The Time Lord hung on as she rumbled like an earthquake, shaking him so hard he was flung off the controls. The Doctor put a red-shoed foot up to pull a lever down, but missed as the TARDIS shook again, this time much harder. The lights went off, and he was surrounded by the oppressive feeling of night. The space ship bounced off something, and the next thing the Doctor knew the lights were on, flickering, and he was hanging on a sharp piece of metal from the ceiling, caught on the back of his suit. He kicked, sending a shoe landing somewhere in the debris below him.

"Oh, come on, girl! Give me a little chance here, would ya?" he asked desperately. The only reply was a deep, threatening growl from the ship. The lights went out once more, and the Doctor was free from the hook as the TARDIS flipped upside down. "If only I could find my sonic," he grumbled. He held on to the railing tightly as she tumbled through space and time.

The doors below him opened suddenly and he lost his grip. The Doctor fell out of the TARDIS, spiraling towards the ground below him. It looked much like Earth, except he wasn't quite sure where. But that didn't exactly matter right now, as he was free-falling to ground that was like ten miles away. Suddenly, the TARDIS came twisting and spiraling towards him. He grabbed the side of it and held on for life as she fell. The Time Lord climbed inside, and clung to the railing again. The ship shook harder, and the doors slammed close. He pulled out of the way just in time as his foot was nearly slammed in the door. The Doctor clambered to his feet, and was thrown forward by a sudden rocking motion. His head slammed on the control panel of the TARDIS and he remembered no more.

* * *

A pegasus blasted through the air, multicolored mane whipping behind her. She smiled, feeling her cheeks tug back, tears coming from her eyes. The barrier was forming; she could see it. She was so close. . .

BAM!

Rainbow Dash's senses were overloaded with pain as something slammed into her, going so fast she didn't get a good enough look at it as it went whizzing by. The pegasus desperately tried to get back in control of her body, wings going out of sync. She ducked her head into her hooves and let herself free-fall for a moment before lifting her head up. The green grass surprised her, but her quick instincts made her wings pop out, sending her soaring back into the great blue sky which was littered with fluffy white clouds. As Rainbow Dash recovered from the pain, she grew angry. She was going to give whoever had run into her a piece of her mind. Or her hoof. Whichever one she wanted. The pegasus spread her wings, angling into a slow dive. Going below the layer of clouds, she was met with a thick cloud of smoke.

"What in the wide, wide world of Equestria?" she asked herself, unknowing of what was even happening. "I swear to Celestia if that's another dragon. . ." She landed, waving her wings to rid her lungs of the smoke. Dash slowly approached the source of the smoke, and found a huge blue box, stuck upside down in the ground. It was on fire, flames licking the side of it like a lizard's tongue. Rainbow shot up into the air and grabbed a cloud. She brought it down to right above the thing and bucked it a few time to release a torrent of fresh rainwater upon it. It sizzled, and the smoke cleared as the fire went out. Dash tapped the side, finding no scorch marks or anything on it. "What? How? This. . . thing! was on fire! It should be burnt to a crisp!" She looked incredulously at it. "And it's wood!"

BANG!

Rainbow jumped back, startled momentarily by the sudden noise from within. The door opened a crack, but as it was stuck in the earth, it didn't really move.

"Oi! Get me out!" a voice shouted. Dash fell onto her haunches, ears flattening as the banging on the doors grew more incessant and angrier; more frantic. There was a pause, followed by the sound of stuff moving around. "Ay! My sonic screwdriver! Found it!" The doors were suddenly opened, earth flying back at the pegasus. She lifted a blue hoof to cover her eyes as a bright light shone from within. A pony, wearing a ragged blue tie, fell out, exhausted. He glanced up, big brown eyes meeting her cerise ones. He jumped up. "'Ello! Can you tell me where I am?" He glanced around, smiling widely for one that had just fallen out of the sky.

"Did-did you just fall out of the sky?" Rainbow Dash asked, pointing upwards, her eyes wide. The stallion glanced up, smile not wavering in the slightest.

"That would be me, then!" he replied, and looked back at Dash.

The last thing he saw was a blue hoof coming at his face.

* * *

Blurred shapes crept past his vision, random colors blending together to finally form the sky blue pegasus in front of him. The Doctor shook his head, blinking furiously for a few moments afterwards. He heard her speak, and perked an ear.

"I asked you, what are you doing here?" she said angrily. The Time Lord grumbled something in return, and from the sound of it to his own ears it sounded more like gibberish than a real response. Obviously he was correct, as a stinging slap across his face brought him to full attention. Her rose eyes burned into him, fire lighting in her gaze.

". . Eh, traveling. TARDIS went all crazy; must've gotten damaged when that laser hit the control panels. Garbudians, ha, such a ridiculous race. Think they'd ever be able to steal her away from me again! This time I was prepared! Though I don't see why I'm a pony, I mean, that was fairly obvious when I grabbed my sonic screwdriver. I had hooves! First transformation to a different species when traveling! Never done that! Quite fun, I must admit. Maybe that had something to do with the TARDIS going all wacko! Was she trying so hard not to let anything happen to me that when we started leaving the Garbudian planet she couldn't do anything else but try to stop my transformation by only focusing her power on me? Was that why? Hmm, that seems about right. She's always been overly protective of me! Ha! Imagine that! TARDIS acting like a mother! Never really thought of that on a bigger level though it seems as though- OWCH! You _really_ need to stop doing that!" the Doctor shouted, shifting a hoof to bring up to rub his face, only to find he was tied against a tree. He pulled on the ropes, to no avail. "Hey, why am I tied up?"

"_I'm _the one asking questions here, not you! Ya got that, ya dip?" the pegasus snarled. She turned around, flicking her rainbow tail in annoyance. "Who are you?"

"I'm the Doctor, who are you? Oh, I mean, um, you are someone and I am the Doctor, right, no questions from me," the Time Lord corrected, catching her glare back at him.

"Doctor? That's it?" She turned around again to look at him fully. "I'm Rainbow Dash, by the way."

"Nice to meet you Rainbow Dash! And, yes, that is it. Just the Doctor."

"Alright, _Doctor_, why were you flying at breakneck speeds towards me?! Why did you smack me out of the air like some little bug?! I was going so fast that I could've been killed in a collision like that! Even I know that! How come somepony with a blue flying box doesn't know that?!" She slammed her hooves on the ground, teeth grinding together. The Doctor folded his ears back, surprised at her fierceness.

"Well, I myself am still kind of wondering. But, don't worry about it. TARDIS really acting bonkers, and even after 900 years of time and space I still can't fly her!" he said, laughing. Rainbow Dash snorted.

"What are you going on about? 900 years? Are you crazy?" she asked incredulously. The Doctor shrugged.

"I suppose I am. That's me-madman in a blue box. But, hey, don't worry 'bout me. No, not at all. Why don't you just untie me and I'll get out of your hair, ay?" He smiled brightly at the pegasus.

"Pfft, no way. I have a right to report you to the authorities. You nearly killed me. With a box. You'll be in jail soon if I have anything to say about it." Dash gave a firm jab to his chest, causing the Time Lord to give a gasp of indifference. He stuttered a few times before he could say anything.

"Hey! If it gives you any consolation, I was just falling out of that box-how long have I been out?" He raised an eyebrow.

Dash looked down at the watch she had drawn on her wrist. She pondered it for a moment. "About, I don't know, twenty minutes since I drew this on." She waved the red ink watch in his face, his eyes following it back and forth.

"And _when _did you draw that on? Before or after you tied me up?"

"Alright, alright. After," Rainbow Dash said. "Around five minutes afterwards."

"Okay, right, twenty-five minutes, and I was trapped in the TARDIS for about five minutes before I came out. . . ten minutes I was trying to get ahold of her. . . so, that means only about forty-five minutes-give or take-I was falling to the ground because she threw me out. So, technically, it wasn't my fault, so technically, you can't take me to authorities because I didn't do anything wrong!" the Doctor finished triumphantly, looking up at Rainbow Dash. She had one eyebrow raised, a smirk on her face. "What? What are you smiling about?"

"Oh nothing, it's just that since you can't even control that box, you are a reckless flier! Which means I can turn you in still!" She grinned, then turned around, smacking him in the face with her tail as she did so. The Doctor grumbled something, fidgeting in the ropes. Rainbow Dash raised her wings, preparing to shoot off. Then, abruptly, she stopped and face him again. "Where are you from, by the way?"

"Let's just say not from around here," he responded coolly. The Doctor eyed the pegasus cautiously.

"Are you a changeling?" Dash questioned, folding her wings again and sitting down in front of him.

"If I knew what that was, would that be bad?"

"Yeah. Pretty bad." She shifted her position. "What are you then? And your box? That thing's wood. I know that. It was on fire; it should've been completely destroyed. Plus, why would anypony in their right mind want to travel in such a small thing?"

"Warranty. That's all. And you'd be surprised. It's actually quite spacious in there." The Time Lord looked around, trying to act unconcerned. The fact of the moment was that he couldn't have any random equine getting any wrong ideas about him. He was sure he didn't want to go to jail. Again. Although breaking out of jail wasn't hard, to him, at least, as he had his extremely handy sonic screwdriver, it wasn't a pleasant place to be located. But, really, could going to jail in a world full of magical technicolored ponies be that bad?

"You know what? I really don't believe that answer. There's something about you; something odd. I don't know what it is exactly, but I'm gonna find out." Rainbow Dash narrowed her eyes, studying the Doctor closely. As her eyes eventually wandered off to something else, he leaned his head down under his collar and grabbed his sonic. He quickly broke the ropes, and jumped up. Dash watched, momentarily stunned, but shook her head and shot off after the escaping stallion. Obviously the Doctor was no match for Equestria's fastest flier, so she quickly caught up to him. He looked over at the pegasus, glanced in front of him, then winced as Rainbow ran face-first into the TARDIS doors with a loud 'thud'.

"Well, see yah Dash! Sorry about your face!" he shouted as he pulled the doors out for once as to make sure the smashed pegasus didn't somehow get inside, stepped inside the TARDIS, and closed the blue doors. He found himself falling onto the ceiling. "What? What? How-what?!" The Doctor glanced frantically around him at the huge mess. "But you have your own gravity! You're upside down out there but you're not supposed to be in here! What is going on with you?" He tried to jump up to the control panels but found it was too high. Growling in frustration, the Time Lord picked his way through the mess. He grabbed his shoe he had lost earlier, with some difficulty, and chucked it at the controls above his head. It caused a few sparks to fly, but then, suddenly, everything turned back right side up. He landed with a bang on the appropriate side of the time traveling ship. "Well, okay then. Fine. Works for me! Come on, let's leave this deranged pegasus behind, shall we?"

The Doctor flipped a switch, and with a shudder, a screech, and a whistle, the TARDIS started to disappear. Sparks flew out of all directions, setting fire to half of the console, but they reappeared, the scratchy sound of the TARDIS filling the late afternoon air. The Doctor stumbled out of the ship, coughing. He grabbed a fire extinguisher and pulled the pin, spraying the control system of his ship to put out the fires. He threw the empty can aside and closed the blue doors, observing his surroundings. The quaint little buildings towered above him, filling the Doctor with a sense of comfort.

"Looks comfy, doesn't it dear?" he asked the police box next to him, leaning against it. He cracked a grin, crossing his arms and standing on his back hooves. He heard a rustling sound, and looked around. A small, round, green bush growing against a house quivered slightly, and saw three pairs of eyes looking back at him. They quickly vanished back into the shadows as they realized they had been seen.

"I think he saw us!" a high pitched voice squeaked. The same voice let out a shrill squeal as he heard a smack.

"Shh! We don't want to him to hear us!" another growled-probably the one that had hit her.

"Sorry!" the small voice replied.

"Girls! Scootaloo, no hittin'. Sweetie Belle, no loud noises. We need to figure out our diagnosis. Ah say crazy-or loco in the coco, as Pinkie Pie would put it," a third voice chimed in, her southern accent thick.

"I agree. I mean, who was he talking to? 'Looks comfy, doesn't it dear?' What a wacko," the one, presumably Scootaloo, agreed.

"He is by that box that I've never seen before," Sweetie Belle added.

"Don't be silly, Sweetie Belle. Who talks to a box?"

"Well, there was that one time you-"

"H-hey! No need to mention that! Just focus on the task, huh?"

"Alright, alright. was just saying."

"You know, it's not nice to talk about someone."

The three ponies screamed, leaping out of the bush, a flurry of leaves scattering over the ground. They pressed themselves against the house on the opposite side, shaking as the Doctor stood up from within the bush. He grinned. "I mean, seriously! Like I didn't see you! Or hear you, for that matter. . . " He grimaced and looked away. "And I'm not a wacko, either! I'm just. . . well, never mind that. You don't need to know." He shook his head to clear it. "What I need to know, though, is where I am. Where are we?"

"You hit your head or something?" Scootaloo asked, sticking her wings out.

"Oh, no, look at me, I'm stupid!" He knocked on his head a few times. "Completely empty in there, I tell you."

"You're in Equestria," Sweetie Belle piped up, pushing forward to stand next to the little orange pegasus, much to her irritation.

"Equestria, you say? Never heard of it. Strange. I've knowledge of nearly everything in the universe," the Doctor said, tapping his chin thoughtfully.

"But didn't you just say you were stupid?" Scootaloo asked.

"Oh, um, yes. Clever one you are. But before we go any farther in discussing my I.Q, tell me the date."

"June 17th, 7086!" the southern filly said, finally participating in the conversation. The Doctor grinned.

"Much later in the future! Very much so!" He knocked on the police box's side. "Good work, girl!" He looked back at the three fillies. He slowly brought his hoof back down to his side. "Eh heh, heh. Um, say, is there a library near here?" Three multicolored hooves pointed left. "Thanks!" He turned around and abruptly ran into a wall. "Very odd, being a pony. Eyes slightly off center." Feeling their eyes on him, he scurried around the corner.

"You're going the wrong way!" Sweetie Belle shouted. He ran by again.

"Right. Thanks Sweetie Belle, Scootaloo, and I didn't catch your name," the Time Lord nodded at the pale yellow filly with the giant bow on her head.

"Applebloom," she said. "And you are?"

"The Doctor. Allons-y!" He sprinted off.

"Still the wrong way!" Sweetie shouted.

"ALLONS-Y!" They saw him run past them once again.

* * *

"Ow. . . ow. . . ow. . ." Rainbow Dash groaned, rolling over onto her back. Her front hurt like crazy; she ran into something pretty hard. She shot up, only to find herself cringing in pain. "That stupid stallion! And his box! That's what I ran into! And now he's gotten away!" The pegasus shook off the pain and leaped into the air, prepared to hunt and hurt the mysterious Doctor. "I am going to find him of it's the last thing I do." Dash shot off, her signature trail marking where she'd been only moments before. _I'm going to murder him! I will! I swear! That mangy little-hey, Scootaloo! _Rainbow took a detour and picked up her little friend, swooping around in a large, sweeping circle. The filly laughed, buzzing her wings as she hoped for a miracle and took off into the air, finally free from her life on the ground. Her arms stretched out and as they neared the ground again, she relaxed. Maybe someday, but not today.

"Oh, man, Scoots, you don't know how glad I am to see you! I had the weirdest and most shocking day! Okay, maybe not as shocking as doing a sonic rainboom and winning the Best Young Fliers' Competition and saving Rarity from certain death but still pretty odd!" Rainbow Dash explained breathlessly. She quickly began telling the story to Scootaloo and her little pals, the Cutie Mark Crusaders, about her strange encounter with the Doctor, and about how as soon as she found him she was going to tear him limb from limb-

"Rainbow Dash, we get it. You don't need to go into detail about how you're going to mangle him," Applebloom said, the CMC members giving a few shudders of horror from what they had just heard.

"Sorry. But he tricked me. And nopony tricks Rainbow Dash and gets away with it. NOPONY!" Her shout rattled the eardrums of every pony in a hundred yard radius.

"Wait a minute. You said 'the Doctor?" Sweetie Belle asked, raising an eyebrow as her voice went up an octave in question. Dash nodded. "Well, then we can tell you about our own encounter with the Doctor. . ."

* * *

"No way! You saw him! And you even know where he went! This is great! I'm going to beat the-"

"RAINBOW DASH!" the fillies shouted simultaneously.

The pegasus smiled sheepishly, ears flattening sides of her head for a moment before perking up again. "Sorry." She glanced at her 'watch'. "Gotta go! The library is calling my name!" She leapt into the air, churning her legs before leaving a few coughing fillies where she had just been in a cloud of multicolored smoke.

* * *

The Doctor rushed along the streets, dodging a light green unicorn and a cluster of flower ponies. He took a flying leap over a fruit stand, surprising the pony selling to the point of which she screamed. He looked around, searching for anywhere that looked like a library. "Well, that makes sense, doesn't it?" He looked up at the giant tree in front of him. "Library in a tree. Really hope the reason I'm here isn't to fight more Vashta Nerada." The Time Lord pushed on the door. It didn't budge. "Hmm, interesting. Wood, too. Blast!" He shoved again, really putting his shoulder into it. The door gave a creak and he found himself falling inside.

A purple unicorn looked up from where she had several test tubes out. "What? That door opens out. How'd you get it to go this way?" she asked, baffled.

The Doctor look back. "Um, I'm good with doors." The sign on the TARDIS, "PULL TO OPEN," flashed in his mind. He shook it off and approached the short purple unicorn. "Um, I'm new here and I was wondering, where are the nonfiction books?"

"Well, hi there. I'm Twilight Sparkle, owner and tenant of this library. Nonfiction's right over there, to your left," she said kindly. "Any type of book you're specifically looking for?"

"Well, Now that you mention it. . . history books. Or science. Or both. Preferably both, if you don't mind." He glanced around quickly. "And I'm the Doctor, by the way. Nice to meet you Twilight Sparkle."

"Doctor who?" she asked as he turned in a circle to get a better look at the shadows. He mouthed the words with her, a smirk on his face.

"Just the Doctor. Now, books." Twilight nodded and led him over to another little room. She levitated a few thick books down to their level from the top shelf.

"Okay, I have four history books right here, but what kind of science book are you particularly looking for?" She set the books down in front of the Doctor.

"Space. Time. Genetic, or, let's see, what do you call that. . . oh yes! Biology! Yes! That's it! Those types," he responded.

"Alright. Well, space is over there-" a purple hoof pointed one way "-and time's over there-" a head nod "-and, finally, biology's over there." Twilight smiled at him. "If you need anything, just ask. Oh, and if I may, can I know what you're working on? I mean, most ponies don't read books like that for fun." The Doctor flipped open the first book of the history and scrolled through it. He looked up at the unicorn.

"Well, now, how to put it. . . part of it is for finding out what made my DNA change and turn me into a pony, and the rest is for fun, really. Might as well, while I'm here, ay?" Twilight stood there, a look on her face of severe confusion. "Ah, I see. Never mind what I just said. You go off and finish whatever experiment you were doing." The pony raised a hoof to leave. "And might I suggest putting the blue-bio-acid into the reticulate-formula. Then mix the hydrochloric acid with the hydrofluoric and put them all together." Twilight looked at him, her mouth open and deep violet eyes wide. "Be careful, though. A little bit of a boom afterwards. Back off. And do not leave it sitting for more than ten minutes, would you? Then I'll have to come in and fix it." He rolled his eyes, snorting. "Typical of other species to do that." The unicorn nodded, her throat dry, and raced out the door, slamming it closed with her magic behind her. The Doctor blinked. "What was that about? Whatever, I must get to reading."

* * *

_**So, how is it so far? If it's absolutely terrible, sorry. First Doctor Who story. I've been watching it. All seven seasons of the new Doctor Who. Anyways, hard to do Time Lord talk. Wasn't exactly sure what to write. . . **_

_**Hope I got the Doctor's personality right. . . and yes, this story will be full of him getting slapped or mauled by Rainbow Dash and going the wrong way. Pretend the library door opens out only, and don't question logic. Speaking of it, don't question anything. Nothing. Twilight's doing her best. Plus: ALLONS-Y! **_

_**And another thing-I won't have the next chapters of Rainbow Chaos or What Happened to Discord! ready for a while. I've been really busy. And I know, I wrote this, and it sucks. . . kinda. But I've no motivation for those anymore. Sorry. But don't worry, they're NOT going to be cancelled. I think WHTD is going to be finished within the next few chapters, though. I need to get that done. If I get a chapter up in the next week, or two, feel lucky. :/ **_

_**Anyways, new story, how do you like it, blah, blah, blah. **_

_**You know what to do. **_

_**~ RandomHamster33**_


	2. Don't Tell Anyone

Rainbow Dash raced through the town, winding around buildings and through crowds of ponies. If she was to get to the library, she was going to do it in style. As she saw the tree house in the distance, she slowed, getting to just the right speed to where she only barely broke the door off its hinges. The smashed piece of wood broke apart, and was flung halfway across the room. Twilight Sparkle barely managed to get out of the way before she was impaled on a shard of it. The surprised unicorn looked over at Dash, who was busy shaking out her mane. She ran a hoof though it and hovered over to Twilight.

"Have you seen a stallion called the Doctor?" Rainbow Dash demanded, grabbing Twilight by the shoulders and shaking her about. The purple unicorn pointed to the other side of the room, where said pony was just walking out of it. His eyes went big and he shot out the empty doorframe, followed closely by the pegasus, who had just dropped Twilight unceremoniously on the floor.

"Stay away from me you crazy pony!" the Doctor shouted, galloping through the streets of Ponyville.

"CRAZY?! You're gonna regret that! And everything else!" she yelled, flying closer to tackle him. As the two sped around the town, three fillies were hearing the commotion and were trying to look for it.

"What do you think it is?" Sweetie Belle asked.

"Um, you might want to look that way," Applebloom said, taking the smaller unicorn's head and turning it the other direction. The Cutie Mark Crusaders watched as Rainbow Dash chased the Time Lord through the streets.

"Ah, I see." Sweetie nodded.

"Come on! Let's get a better view!" Scootaloo told them, hopping onto a barrel. She motioned with her hoof for them to follow. The small pegasus buzzed her wings, lifting herself just enough to get herself to the edge of the roof of a house. She hauled herself up, and then turned to help Applebloom and Sweetie Belle.

"So, basically we're going to watch somepony get beat up?" Applebloom asked.

"Yep!"

"Sounds good." They got comfortable and Sweetie Belle pulled popcorn out from behind her.

"Uh! Where did I park the TARDIS?!" the Doctor wailed, running down yet another street in vain attempt to find the spacecraft.

"Your box won't save you from the wrath of my hoof this time!" Dash shouted.

"That **box **is the best ship in the universe and if you think it won't stop me from getting punched in the face by some crazy equine, then you better be happy I'm not a violent person!" He took a flying leap across a small stream crossing through town and disappeared down an alley. Rainbow rounded the corner and stopped abruptly.

He was gone.

"For the love of Celestia!" she yelled, throwing her hooves into the air in outrage. She landed and started to search through the various bushes clustered around the houses. The pegasus huffed angrily, smoke coming of her nostrils she was so angry. She should've just beaten the fudge of him right when she saw him, not chase him through town, playing a cat-and-mouse game of tag. "If you don't come out I will. . " She stopped, not sure what to threaten him with. "I'll. . . uh, fine! Forget it!" She angrily flew off, going to search for Scootaloo. As she disappeared into town, the brown stallion suddenly appeared. He coughed a few times, dropping the sonic screwdriver on the ground as it burned him. He examined the burnt pattern in his hoof and glanced down at the probe. It was destroyed; the cloaking device he had put on it wasn't developed for it yet. He would have to work on that.

"Great. Just fantastic. No screwdriver, and an insane pegasus after me. Good job, Doctor, for getting yourself into this mess," the Time Lord muttered to himself. He kicked the burnt out probe into the bushes then hurried off, the burning sensation in his hoof driving him back to the TARDIS. The Doctor scurried about, searching for the space ship. He eventually found it, sitting exactly where he left it. When he got inside, he rummaged around in a bin underneath the paneling of the floor. His only first-aid kit was in here, as usually his injuries weren't that severe, and if they were, well. . . he knew what happened then. He rubbed some ointment on it and bandaged it, then went to work fixing the TARDIS. She was still buzzing randomly, sparks falling from the ceiling as she tried to heal herself. The Doctor stroked her console, then pressed his face against it. "Shh, shh, it'll be okay old girl. Everything's fine now; well, hopefully. Once I get a new sonic screwdriver, I'll do a quick scan of the area. You always bring me to where I need to be." The screen flashed on and off, making the Time Lord pull away from the console. It was dark already. He turned away, going to go get do some more research.

What he didn't notice was the blonde girl yelling at him from the repeatedly flashing screen.

* * *

"So, any luck?" Scootaloo asked her idol, who was busy drinking a milkshake angrily at the other side of the table. Rainbow Dash released the straw from her mouth, leaning back against the bright pink chair.

"No. I was so close, but I messed around and didn't get him," she replied, shifting her wings as she leaned forward again, sipping her chocolate-fudge-caramel-mint-birthday cake-coconut-banana-chip milkshake. It was a flavor she herself had made up one day. She had just broken her wing and Pinkie Pie wanted to make her feel better. She had told Dash she could design any kind of milkshake she wanted, and that's when the chocolate-fudge-caramel-mint-birthday cake-coconut-banana-chip milkshake was born. Now whenever she was having a bad day, Sugar Cube Corner was where the pegasus went.

"Oh. I mean, bad for you, good for him, as he probably didn't want to get injured," Sweetie Belle observed. She held out the bucket of popcorn from earlier, offering some to Dash. She reached forward and took a hoof full, throwing it into her mouth in one swift motion.

"I don't care whether or not he doesn't want to hurt. It is going to happen, no matter how long it takes." Rainbow stretched her wings, putting her back hooves up on the table, front hooves behind her head. She took a deep breath and closed her eyes.

"Is tomorrow's flying lesson still on?" Scootaloo asked, sitting up in her seat eagerly.

"Of course! Searching for the Doctor is just a hobby." She waved a hoof through the air absent mindedly, then fell asleep.

"Well, what to do next?" Applebloom asked, leaping out of her seat.

"How about Cutie Mark Crusaders Cave Explorers?" Sweetie Belle suggested. Scootaloo and Applebloom glanced at each other.

"CUTIE MARK CRUSADERS CAVE EXPLORERS YAY!" the three yelled, clapping hooves.

"Keep it down you crazy kids!" an older mare shouted back, hobbling out of the store as her ears pounded.

* * *

"Come on, please?" Applebloom begged, putting her front hooves together as she pleaded. Applejack looked down at her younger sister, a frown on her face.

"Ah don't think that'd be safe for you," the older mare told her. She walked off towards the next tree.

"We'll be careful! There are three of us! It's safe!" The fillies then stacked themselves in pyramid formation, getting up to Applejack's height. Applebloom squeezed her sister's cheeks together, looking into her green eyes. "Come on! It's fine! PPPPPLLLLEEEEAAAASSSEEE?"

"Ahhabuhm, het gur uf mah fsh." She pawed at the small yellow hooves on her cheeks and stretched her jaw by opening her mouth widely. "Better." She bumped Applebloom onto her back and bounced her a few times.

"Applejack! Please?"

"Yeah, AJ, please?" Sweetie Belle asked.

Scootaloo fluttered her wings, hopping around. "Pretty please with apples on top?" Applebloom jumped down next to her friends.

As she looked down at the three wide eyed fillies, she sighed. "Fine, you can use the old cave equipment. It's a little dusty. We haven't used it in a while. Be careful."

"YAY!" they cheered. Applejack cringed. They started running off towards the old shed, their voices getting softer as they disappeared through the trees.

* * *

"Hurry Applebloom! We need to leave before three!" Scootaloo called from outside the store. They were sitting along the wall of the hardware store, waiting for Applebloom to get some more supplies.

"Just a moment!" the filly called back.

As they waited, Sweetie Belle kicked a rock around. She hit it into the bushes, and went to get it. "Sweetie, it's just a rock!" Scootaloo watched as the small unicorn rummaged around in the leaves looking for it.

"But I like it! I think I'll keep it," she said, lodging herself farther into the bush. Scootalo sighed and leaned against the wall, crossing her hooves over her chest. "Whoa! Scootaloo, take a look at this!"

"What? Another rock?" The pegasus fell back down onto all fours only to have something skinny and silver pushed under her nose. She grabbed Sweetie's hoof and brought it lower so she could she whatever she was holding. "_What _in Equestria is that?"

"I don't know! How should I?" Sweetie Belle grunted, puffing her cheeks out. Her horn sparked, and the magic flowed through it, picking up the strange object and hovering it in mid-air.

"You know, it's been really useful, you finally learning how to use magic." Scootaloo examined the skinny thing floating in the air. "Have any ideas?"

"No."

"But you're supposed to be the smart one!"

"I have a large vocabulary, that's pretty much it. Applebloom's the math whiz. And I reckon that this is something math-y!"

"I don't know. Looks more science-y to me."

"What looks science-y?" Applebloom asked as she came up behind the two. As the object was suddenly flung at her, the filly dropped her bag of tools.

"Oops, sorry. Hard to use this thing still," the unicorn apologized. She picked it up again, green magic fizzing before settling to a constant shifting aura.

"What is this?" Applebloom raised an eyebrow.

"We have no clue."

"It looks all space-age-y though," Scootaloo said.

"Kinda like a pen," Sweetie Belle added.

"A weird pen? Seems a bit too advanced for a pen. And it has a bunch of buttons," Applebloom pointed out.

"Yeah. . . ooh, I know!" The two other fillies looked over at Sweetie Belle, who was bursting with excitement.

"Well?" Scootaloo prompted, rolling one hoof in the air, beckoning for an answer, which seemed to be stuck on the unicorn's tongue.

"Get on with it girl!" Applebloom yelled.

"F-future! It comes from the future!" Sweetie shouted. At her excitement, her magical concentration shifted, and the object wobbled in the air. "I mean, look at it! Futuristic looking, right?" She developed a more serious tone. The sun shifted in the sky, causing Sweetie's face to be cast in shadow. "Aliens."

"Aliens? In Ponyville?" Applebloom deadpanned. She glanced at Scootaloo, one eyebrow raised. The pegasus shrugged.

"Think about it though. Random, weirdo pony who doesn't know where he is, what _year _he's in, appears out of nowhere with a really tiny blue box! Doesn't it seem alien to you?"

"Sweetie Belle, are you implying that the Doctor is an alien?" Scootaloo asked. Sweetie nodded furiously, unable to talk anymore because of her energy. "Applebloom?"

"Um. . . it does seem kinda odd, if you really think about it," the filly answered.

"Okaaaayy. . ." Scootaloo nodded slowly, trying to think. "You know what? I think we should go and talk to the Doctor!"

"CUTIE MARK CRUSADER ALIEN HUNTERS YAY!"

* * *

"Just shift the temporal balance. . . aha! There we go! All fixed up! Good to go! Now, new sonic screwdriver. Must get that done," the Doctor said to himself, hurrying about the TARDIS to get things accomplished. He pulled a few levers, pressed a few buttons, and rolled a little ball. A small sound was heard, and the words "SONIC SCREWDRIVER: 0% COMPLETED" appeared in Gallifreyan on the small screen. The Doctor smiled and stood right next to the console, waiting. After about a minute he grabbed his head, groaning. "Ah! I can't wait here any longer! How much left?" He looked at the screen. SONIC SCREWDRIVER: .1% COMPLETED. The Doctor groaned and let his head flop onto the console. "Ouch." He picked his head up and looked around. Then back at the screen. Then around the TARDIS. Then back at the screen. He tapped his hoof furiously on the console, biting his lip. Then he threw his arms up, crying out in frustration. "I can't take it anymore! I've got to do something!" Flying towards the door, he reached for the handle-only to find himself on the floor with a hurt nose because he was going to fast, and his vision was off. "Darn pony sight!" He leaped up, went for the handle again, and threw the door open.

He was immediately met with the sight of three fillies at his doorway.

The Doctor hopped back, startled. He quickly positioned himself so that they wouldn't be able to see inside his TARDIS. "What do you want?"

"Have we ever told you that you have a really funny accent?" Sweetie Belle asked.

"Oi! Watch it!" He glared down at the fillies. "So, tell me, what do you need?"

"We wanted to know if you were an alien," Scootaloo said. Applebloom quickly put her hoof over the pegasus's mouth and smiled.

"Uh, what she meant to say was, um, hello?" Applebloom lied, her voice increasing in pitch.

"Right. . . bye!" The Doctor slammed the blue door in their faces, and leaned against it. His eyes went wide and he took a deep breath. "No, no, no, no! We can't have these fillies knowing! Okay, I'll have to play it cool." He was about to open the door again when he realized his tie was ripped. "Hmm. I think it's time to change." He flicked open a box and searched through it, finding a new tie and collar. He slipped them on, tightening the knot. The Time Lord looked in a mirror, checking out his pony form. He ran a hoof through his mane, stopping at his sideburns. "Well, don't think you see many ponies with sideburns, but oh well." He sighed. "Still not ginger. Blast!" Glancing at his tail, he saw an hourglass on his flank. "Ah, this cutie mark I read about. Suits me. Time Lord-hourglass." He pondered it for a moment. "Yep, suits me." The Doctor finally opened the door, and saw the fillies still sitting there. His ears fell against his head. "And I was hoping you'd gone."

"Why'd you leave, hmm? Nervous we found out your secret?" Scootaloo questioned. The Doctor looked at her.

"What secret?" He quickly left the TARDIS and closed the door before they could get a good look inside.

"You know, the you being an alien."

"I don't know what you're talking about." _Uh why am I scared about three little fillies thinking I'm an alien? Kids are very imaginative. _

"Oh yeah? Sweetie Belle, show him the thing."

"Alright. Here it is," she said, holding up the screwdriver with her magic. The Doctor's breathing hitched, surprised at seeing the thing he had just kicked under some bushed earlier today.

"Where'd you find that?" he demanded, a little too harshly.

"Oh? Recognize somethin'?" Applebloom asked slyly.

"N-no!" _Blast! Stop stuttering, you idiot! These are children! They don't know what they're talking about. . . But they've deciphered enough to know that **YOU ARE **an **ALIEN. **AH! Voices inside my head, stop arguing! _

"Are you sure about that?" Scootaloo probed.

"Yes! And I would know because even if I was an alien I probably wouldn't know what a sonic screwdriver is!" He took a step, then stopped. _Oh my god what have you done. You **MORON. **_The Doctor face hoofed himself, groaning loudly. "Why would you do that you stupid brain."

"You're an alien! You're an alien!" Sweetie Belle shouted, bouncing around.

The Time Lord quickly put his hoof up to his mouth. "Shh." The unicorn suddenly stopped, confused.

"You're actually an alien, aren't you?" Scootaloo asked quietly.

"Yes, yes. I am, okay? But be quiet. Tell no one or you'll get me killed. Or worse-you'll get them killed. Now shut up and give me that." He swiped the sonic screwdriver away from the pegasus, despite her objections, and stuck it under his collar. He would need to dispose of it later, inside the TARDIS. "Now, leave me alone." He turned to walk away.

"How can we leave you alone now? We've been talkin' to an alien this whole time and we didn't even know it," Applebloom said.

The Doctor spun around, a look of anger in his eyes. The fillies stepped back, wary. "Listen to me." They stayed silent. "If you follow me, or tell anyone, you will get yourselves hurt. You'll put this whole town in danger. You got that?" They didn't move. "Good." He started walking again.

"What about your ship? The, uh. . box," Sweetie Belle mentioned.

"The TARDIS? Nothing. I'm not telling you anything about me. I know how kids are. No species understands." He went faster, trying to get as far away as possible.

"Tell us!" Scootaloo shouted. She looked around and grabbed her scooter, which was laying against the wall of a house. She hopped on, pulling the two other fillies in the wagon that was attached to it.

"Are you three trying to get killed?! Forget I was ever here!" The Doctor was sprinting now, not wanting to endanger the lives of others everywhere he went. But Scootaloo was quick on her scooter, and she easily stayed level with him. "Oh for Pete sakes!" He came to a sudden halt, making them shoot off ahead of him. The Time Lord turned back, running for the TARDIS as if he was trying to escape from Cybermen. Upon reaching his ship, he pulled a few levers. He was going to have to leave this area. The TARDIS wheezed, disappeared, and rematerialized across the town. He was now somewhere near a forest. "Finally. Just have to be careful not to let anyone find me." The Doctor quickly checked how far done the sonic screwdriver was, and chucked the old one unceremoniously across the control room. SONIC SCREWDRIVER: 45% COMPLETED. "Still quite a ways." He left the ship, checking both ways, and vanished into the long grass.

* * *

"Great. We lost him," Scootaloo muttered. She kicked a rock into the stream, angry. "I should've stopped faster." The three fillies were sopping wet from falling into the water.

Applebloom scrubbed a towel over her head, drying her mane. "It's okay Scoots. It wasn't your fault. He stopped suddenly." She tossed the wet towel into the grass.

"Yeah, but now his ship is gone." Scootaloo buzzed her wings, flicking water off them and into the dirt. "We might not find him again."

"Don't worry. We still have that, uh, sonic screwdriver thing. . -y," Sweetie Belle said.

"Uh, Sweetie Belle, he took that."

"He did?!" Her voice cracked. "Great! Now what're we gonna do?"

"We could. . . tell Rainbow Dash." The other two fillies looked up at the pegasus, appalled.

"But he said we would get them killed!"

"He also said that we would get ourselves killed. And we're not dead are we?"

"Well, no, but that doesn't mean it can't happen," Applebloom said.

"What else could we do? Besides, nothing defeats Rainbow Dash!" Scootaloo jumped in the air, striking a heroic pose.

"That is true," Sweetie Belle pointed out. They looked at Applebloom, who sighed in defeat.

"Fine. But we need to be careful," the earth pony told them.

* * *

Rainbow Dash spit her milkshake all over the table. She had slept for a while and then woken up when the fillies came to talk to her. She had ordered another one. But right now, it was all over the table and the CMC's faces. Dash wiped her mouth off. "Are you kidding me?! He's an alien?!"

"He is! We swear!" Scootaloo exclaimed. The fillies all crossed their heart. Rainbow coughed a few times, pounding on her chest. Some of that milkshake had gone down the wrong pipe. Pinkie Pie quickly sped over and wiped the table down, and bounced back to the kitchen.

"Well, what are we gonna do about it?" Applebloom asked.

"How am I supposed to know! If he is an alien he could have a whole torture chamber inside that box! We gotta handle this with caution," Dash said, tapping her hooves together thoughtfully.

"Say, could you plan, and we go cave exploring? We were going to do it earlier, but got sidetracked," Sweetie Belle mentioned.

"Right, yeah. You girls go." The CMC went off, leaving the cyan pegasus sipping her milkshake.

* * *

"This cave look good?" Applebloom asked, motioning towards the giant black abyss in front of them. The CMC stood like ants in front of the entrance, looking in awe at the cavern.

"Where did you learn of this?" Sweetie Belle asked, looking at her friend in question.

"Nowhere. It's always been here."

"Does anypony else know about this?"

"Ah don't know. Probably."

"Good enough for me!" Scootaloo cheered, and, making sure her rope was secure, jumped face first into the abyss. Applebloom shrugged, then plunged into the cave. Sweetie Belle squeaked, eyes filled with fear. She swallowed, then fearfully tugged on her rope. She stood at the edge.

"But. . . it looks scary." Sweetie shook her head. She wasn't going-

Something pushed her in.


	3. SYMPTOMS

Rainbow Dash flew over the layers of clouds, doing a simple morning routine that she did everyday. It was almost time for flying practice; not hers, but Scootaloo's. She was getting so close to actually flying that she could hold herself off the ground for about a minute at the most. Which is a huge accomplishment, especially for a filly that can't fly at eleven years of age.

So, nearly every other day, Rainbow Dash helped Scootaloo develop her wing muscles to fly. She had about, say, ten minutes, so she could complete her exercises. The light blue pegasus finished her spinning motion, and landed on a high cloud. As her last warm-up, she always finished with a show. And that was exactly what was going to happen now.

Rainbow Dash stood at the edge of the fluffy white puff, looking down. She turned around, and positioned her back hooves where they were barely on the cloud. The wind rippled her mane. She closed her eyes, taking a deep breath. A sense of calm washed over her, which was quickly replaced with adrenaline as she dropped off the edge of the cloud. The pegasus fell, her wings pressed firmly against her sides. She went into a streamlined pose, still upside down. She burst through the layers of clouds as she descended. Then, she started spinning. Her signature trail followed her every move, making DNA looking swirls. She was getting close to the ground now. She could feel it.

Pegasi have their own special abilities, like those of unicorn and earth ponies. One of them is the well-known ability to walk on clouds, and control weather. But there are several others. The ability to tell how close they are to the ground is one. Pegasi can feel the change in air temperature, and the level of oxygen in the air. They have to be focused though, which is hard for some pegasi. Rainbow Dash was fairly good at this, when she was thinking about it, anyways.

Rainbow Dash focused. Her breath slowed as everything seemed to happen in slow motion. She pictured the ground in her mind, making a mental map of where she was. And now it was time. Her eyes shot open, and her wings flared out, as she twirled along the very tip-top of the blades of grass underneath her. She held her pose, hooves in front of her. She corkscrewed through town like a bullet. Being so agile, it was easy for her to weave among the crowds of ponies, even at the speed she was going. But she really didn't fell like stopping. She could pull it off. So Rainbow Dash angled her wings so she went into the air. The barrier formed, pulling her cheeks back, and sending her eyes watering. As she climbed higher, frost started forming on her body. She usually never went this high, but she hadn't been going the speed she needed to when she was down at the ground. But she still did it. The sound barrier broke, and she carried the color through. Dash quickly doubled back, going into a quick dive as not to strain herself. She slowed as she reached the last layer of clouds. The cyan pegasus folded her wings in upon hitting the ground; it was time for her lesson with Scootaloo.

Rainbow Dash trotted around the small little park. It was a nice place, perfect for picnics and games with the family. Or in her case, teaching her favorite fan how to fly. The few ponies there waved at Dash, smiling and commenting on how they loved her performance this morning-even better than the one yesterday. With a thanks and nod, Rainbow fluttered her wings, carrying herself away from the others to wait for Scootaloo. The pegasus settled down on a rather large tree branch and pulled a pillow and blanket out from the leaves. (She kept them lots of places, in case of nap emergencies. Pinkie Pie taught her that). She fluffed the pillow and set it under her head, then got comfortable. Might as well catch up on some sleep that she doesn't need while she's waiting, right? Within a few minutes Rainbow was snoring softly, hooves tucked under her head.

All the while, the sun was sinking in the distance. No eager little filly turned up.

* * *

"Sweetie Belle! Come downstairs for breakfast!" Rarity called, her face lifted up towards her sister's room, eyes closed. The white unicorn waited at the bottom of the stairs patiently. After a few minutes of just standing there, she sighed. "Sweetie Belle! Time for breakfast!" No reply. Huffing, Rarity traveled daintily up the stairs. She swung her younger sister's door open and looked around.

It was empty.

Rarity started trembling. "S-Sweetie Belle? Are you here? This isn't funny." She took a step forward, the floor creaking slightly under her hoof. Using her magic, Rarity lifted the edge of the comforter off the ground, revealing what was under the bed. Just a bunch of old boxes and forgotten toys. The fashionista dropped the light green blanket, stepping back. "Sweetie? Are you playing another trick on me?" Rarity's voice cracked. She threw back the sheets on the bed, uncovering a few stuffed animals. She tossed the pillows off the bed. A journal. Rarity looked at it, biting her lip. She pondered looking at the latest entry, wondering if she would perhaps find something about her sister's whereabouts. She levitated the faded blue book up to her face, flipping through the pages. As she did this, she heard a shuffling sound. Rarity froze, heart pounding. She dropped the journal, looking with the corner of her eye. The closet door squeaked. The shaking white unicorn turned around. Her blood ran cold. She got a gentle grip on the handles. . . and pulled.

A large amount of papers fell out, covering the fashionista, who jumped and stifled a scream. Rarity gave a small sigh of relief. But there was still no sign of her sister.

"Sweetie Belle? Please come out. If this is about making you eat your peas, I'm sorry!" Rarity checked the rest of the room again. Nothing. Glancing once more at the journal laying flat on the floor, Rarity swallowed. Maybe she was wrong. Perhaps Sweetie Belle just went and stayed at her friend's house without telling her again. Maybe. But still. It floated up to her height, and she found the last few entries.

**Dear diary, **

**today is gonna be great! I'm going to hang out with Applebloom and Scootaloo after school today. We're going to try and get our cutie marks in spying. Gotta go. Bye.**

**Sweetie Belle**

**Dear diary,**

**today was weird. We met this wacko stallion. He calls himself the Doctor. He talks to his box. He called it 'dear'. I guess it's a girl then. He's really odd. I like him. (He has sideburns)! I wish I had sideburns. :) There's one thing that makes me kinda worried, though. His box just appeared. It made a weird noise. It's blue. Oh, and another thing: Rainbow Dash wants to hurt him. Really bad, I guess. We stopped her before she could explain all she was going to do to him. He also wears a tie and says weird words. He said something along the lines of allenzy and I don't know what it means. Did I mention he didn't know where he was?**

**Applebloom and Scootaloo and I are going to be cave explorers. We're going to ask to use Applejack's old cave stuff. I don't know why she has it, but I guess she had a friend or something. **

**Sweetie Belle**

**Dear diary,**

**OMG! I found this thing under a bush. I think it's alien. I think it's connected to that Doctor. We're alien hunters now. Wish us luck!**

**Sweetie Belle**

**Dear diary, **

**he is! The Doctor is an alien! He admitted it! I was right! :D He said not to tell anypony because it would get them killed. He also said we shouldn't talk to him anymore or we could get killed. He said to forget he was even here. But how could I forget if I just met an alien! **

**We're leaving now. Cave exploring! **

**I'm so glad we stopped by the boutique so many times so I could write in here. **

**Sweetie Belle **

Rarity dropped the journal, frozen. She took a deep breathe. Then she screamed.

* * *

"Hey, Big Mac, have you seen Applebloom?" Applejack asked as she came up behind the large red stallion. He shook his head.

"Nope," was his only reply. The southern mare pawed the ground, gritting her teeth.

"Great. Well, Ah better go find her. Seeyah later." She trotted off, heading towards the entrance of the farm. Applejack walked the dirt road all the way to Ponyville like she did nearly everyday, going at a fairly easy pace. She knew Applebloom usually was gone by the time she was done with apple bucking, but usually not so long. Speaking of it, she hadn't even seen the filly come home the previous night. . . She'd just assumed that her little sister had gone to bed, tired from the day's events.

Deciding to stop at Carousel Boutique in case Applebloom was hanging out there, Applejack turned down a different road and ended up at the door of the fashionista's store. As she raised her orange hoof to knock, a scream cut through the air.

"Rarity! Hold on, Ah'm comin'!" The earth pony threw the door open and raced up the stairs, searching for the unicorn. Rarity stumbled down the steps, her face one of pure panic. She didn't see the other mare coming up the stairs, proceeded to run into her. Applejack, being quick, grabbed Rarity's waist and pulled her back to her hooves before she fell down the stairs. The unicorn held onto her friend, breathing heavily. She then looked up.

"Oh! Applejack, darling! Have you seen Sweetie Belle?!" Rarity exclaimed, placing her front hooves on the earth pony's chest and pushing her face a little farther away from her.

"No. In fact, Ah was just searchin' for Applebloom. Ah wanted to see if she was here," Applejack explained, letting go of the unicorn.

"Applebloom's missing too?! Oh dear! Quick! We must find Rainbow Dash!" Rarity shot down the steps and out the still open front door. Applejack took off after her, finding it hard to catch up at the pace the unicorn was going.

"What's goin' on, Rares? Sweetie's missin', and Applebloom, so why go to Rainbow Dash?"

"Oh, Applejack, you're so thick! Don't you see?! Scootaloo is always around Dash! Maybe she'll know where they are!"

"Oh, Ah see. But there was no reason to call me thick."

Rarity didn't respond as they saw a cyan blur flash overhead, rainbow trailing behind. "RAINBOW DASH!" The pegasus looped around and landed expertly beside them. Her face was sweaty, and she was breathing heavily.

"R-Rarity! AJ! Oh, man, please tell me that one of you have seen Scootaloo! I've looked everywhere! And I know she'd never miss one of our flying sessions," Rainbow Dash said breezily. Her head dropped as she tried to get more air to her lungs.

"No. And we have our own problems. . ."

* * *

"THAT SORRY EXCUSE FOR A STALLON! I'LL RIP HIS HEAD OFF! I'LL KILL HIM UNTIL HE'S DEAD!" Rainbow Dash roared. Her eyes flashed red as if tiny fires were igniting within them. In a flash, she vanished, a cloud of rainbow smoke telling them she was once there.

"We better tell the others," Applejack said with a sigh, shaking her head.

"Agreed," Rarity replied. The two mares ran off, going to gather the other Elements.

* * *

"This makes no sense," Twilight Sparkle said, refusing to believe anything the other two mares were telling her. She simply could not accept this. "There are no such things as aliens, and why in the wide, wide world of Equestria would one come here?"

"We don't know. But that's what Rainbow Dash told us. And even the fillies know. They said he admitted it. But he also said that they would get killed if they told anypony. So that makes it very likely that he is responsible for the disappearance of our sisters," Rarity explained. She was barely keeping calm, and she was really dying on the inside. If her precious little Sweetie Belle was really gone. . . she didn't know what she'd do.

"No. Illogical." Twilight crossed her arms defiantly.

"Oh, for Celestia's sake! Twilight, Ah don't care if you believe it or not, and frankly, Ah still don't know if Ah believe it, but mah sister's gone! And if this pony is responsible for takin' the fillies, then consarnit! Ah'm gonna help in anyway Ah can!" Applejack exclaimed. She stomped her hoof on the floor.

"Come on Twilight! We have to get those kids back!" Pinkie Pie burst out, hopping in place.

"Yeah, I agree. I just couldn't bare to think about it if they were hurt," Fluttershy squeaked. Twilight looked around at the mares, and the looks of hope on their faces. She sighed.

"I guess. . . I guess I can put my science aside. But as of the moment, we need to find Rainbow Dash and help her!" Twilight shouted, jumping up from her spot on the carpet. The ponies all clapped hooves in the middle, cheering. "Let's go!"

* * *

The Doctor popped his head up, angling his ears forward. He couldn't risk anybody seeing him. He was dangerous, and he knew it. Death and destruction followed him wherever he went. Even in a quiet place like this, he knew anything could happen. Something bad was going to happen; he could feel it. The TARDIS sensed it, using her telepathy to send little distress signals to him. She never did that, well, not very often at least. The last time she had done it was. . . he didn't want to even think about it. The Time Lord shuddered, feeling a particularly strong pulse come from his ship. She was very distressed. And to make matters worse, something was happening to him. He wasn't supposed to be a pony. His DNA was altering; he wouldn't even be alive anymore if he was here long enough. The change was killing him.

He had first noticed these symptoms yesterday evening. Small things; the way he thought, his hearts-the beats were slightly off. Even his memories. They were dissolving. Some things. . . Rose. Rose, yeah. He was forgetting. Who was he before? He was Ten, right? Wait, Nine? No, that was fantastic. . .

He was broken from his memories as the TARDIS prodded him with her telepathy."Don't worry, old girl. I'll do what I can," he whispered into the air, not to her, but to reassure himself. This was going to be bad, whatever it was. The Doctor's one and a half days here weren't giving him any information. There were no clues as to what was wrong. No strange occurrences, well, except for him. He had questioned several ponies. They hadn't reported anything odd.

The one good thing was that Rainbow Dash or the fillies hadn't found him. Yet. That probably wouldn't last much longer.

"I'M GOING TO KILL YOU!"

His streak was over. The Doctor looked up. He saw a bright blue bullet coming at him. "Oh no, not her again!" He turned around and galloped away. But this time Dash wasn't playing any games. The Time Lord was bowled over in a matter of moments. The pair rolled a few yards before Rainbow finally got him pinned down. She had a rope in her mouth. He struggled, but without his sonic screwdriver, he couldn't do much. This pony was strong. Usually he was against humans or aliens that didn't tackle him. And especially not from the sky. The pegasus, once the Doctor was tied up nicely, picked him up in her arms and took to the skies again.

"You've got some explaining to do, pal," Rainbow Dash hissed in his ear as they flew.

"Well, fine, if it's information you need," the Doctor said. "Where are we going?"

"That's for me to know and you to find out."

"The library?"

"Well, yeah, but-" She stopped. Then, smiling smugly, she looked right into his face. They stopped flying.

"What are you doIIIINNNNGGG!" He was dropped. He was now free-falling, tied up, and nearing the ground. "Hey, second time falling to my death in two days! New record!" He made a note to give himself a treat for this one. If he survived. He doubted this pegasus was a killer, but she did say she was going to kill him. He pulled against his ropes in vain. Suddenly, Dash was hovering next to him. She casually flipped over onto her back, hooves behind her head.

"'Sup."

"Would you be so kind as to stop me from plummeting to my doom!"

"Why should I?"

"WHY SHOULD YOU?! ARE YOU KIDDING ME?!"

"Nope." She did a lazy flip. Then she held her wings stretched out, parallel to the ground, and just glided in wide circles around the falling stallion.

"Please?"

"Ha! GAAAAYYY~"

"Really?!"

"Okay, okay, fine. Come on." She shot down to near the ground and hovered under the Time Lord. She caught him in her arms and flashed a smirk at him, winking. She then tossed him into the air.

"AAAHHHH!" Dash lazily went up and plucked him right out of the air. "WILL YOU STOP?!"

"Yeah, only 'cuz we got somewhere to be." And in the blink of an eye, they were off again.

* * *

"So, we ready?" Twilight asked, surveying the small group of ponies in front of her. Applejack tossed her apple in the air and caught it in her hoof again, grinning. Pinkie Pie grabbed her party cannon from her mane and smiled happily. Then she gasped.

"Almost forgot!" she giggled, putting a bright white-and-baby-blue helmet on Fluttershy's head and sticking her in the cannon. Her pink hair puffed out as it was stuck on. The pegasus squeaked, her hooves holding the lip of the cannon. Rarity was busy shining her hooves. . . with a nail file that turned into a knife.

"Whoa, Rarity! Where'd you get that?" Twilight exclaimed, pointing at the weapon. The ponies started at it, appalled.

Rarity shrugged. "Just a little shop downtown. But never mind that! We have a filly-knapper to catch!" She smacked her hooves together. The group roared in determination, even Fluttershy getting up to a loud whisper. Twilight lit her horn, preparing to open the door (which she had fixed), when something fell in through the ceiling.

"Sorry! Lost my grip!" Rainbow Dash shouted from outside. Five pairs of eyes went to the pony that had fallen in. The brown earth pony stallion groaned, breaking some of the ropes that were restraining him. A few had been cut when he'd been dropped.

"Being dropped through a library ceiling by a blue pegasus when I'm a pony. . . That's new," the Doctor commented, sitting up as he shook the remaining ropes off him. The surrounding ponies stared in shock, mouths open. The Time Lord glanced around, nodding as he stood up. "And now I'm surrounded. By. . . magical ponies. Also new."

"Hiayh!" Rainbow Dash let out a shriek as she kicked the door down, knocking the Doctor off his hooves and sending him slamming into a wall. The Time Lord slumped over, unmoving. Dash sniffed, cracking her neck. "That's how we do it." She turned to her friends. "So, there you have it. Alien. Boom!" She jumped into the air on the last word, pointing her hoof down at him.

"He looks like a regular pony to me!" Pinkie Pie announced after a few moments of surprised silence. She bounced over to the motionless stallion and proceeded to poke him. Repeatedly.

"Pinkie Pie!" Twilight exclaimed, using her magic yank the earth pony back. The unicorn then studied the Doctor, rubbing her chin with a hoof. "She's got a point. He looks normal. Are sure the fillies weren't just imagining things?"

A look of doubt flashed across Dash's face. "Well, I. . ." She looked away.

"So he's probably a totally regular pony. He's just from a different town." Twilight sighed. "Should've known."

"Oh, the poor, poor, little baby," Fluttershy cooed, sitting next to the Doctor and holding him. She had climbed out of the party cannon, flung off her helmet, and approached the stallion. "You should've known better, Dashie. He looks so sick." It was true; he was paler than he was than when he had arrived. His hearts weren't in the right beat. The changes were becoming more prominent by the minute. Rainbow Dash messing with him earlier hadn't helped things.

A small groan escaped his lips, and suddenly he jerked away, hitting his head on the floor. The Doctor was gasping for breath, lungs weak. "Oh, no, stay still, please." Fluttershy looked up at Twilight. "Can you get me an icepack? He's burning up." The pegasus laid her hoof on his forehead, pulling it away as she felt the heat.

"Yeah. Here," Twiight said, making one appear and giving it to Fluttershy. As she tended to him, the five other mares spoke quietly among themselves on the other side of the room. "Great. Now we've got a sick pony on our hooves."

"But-" Dash started.

"No. Rainbow, the fillies were wrong."

"But where are the fillies? They're. . . still gone!" Rarity exclaimed, starting to cry. Pinkie Pie let her cry on her shoulder.

"I don't know." Twilight shook her head.

"We've gotta find them! We should contact the princess," Applejack suggested.

Before Twilight could say something, a shout from Fluttershy made them go running to her side.

"Girls, he's talking nonsense. It looks like he's been sick for a while," the timid pegasus told them. The Doctor laid on his back, muttering.

"One, no, Seven! No. . . Ten! Ten! Gah!" He shuddered violently as he cried out. "Fantastic! Allons-y! Bananas. . . are good. . . Captain Jack Harkness. . . TARDIS. . . Sarah Jane. . . Who am I? Not. . . human. . . Never. . ." His eyes opened suddenly and he sat up. The ponies shrieked and stood back. His heart beats returned to normal and his color came back. Gasping, he pounded on his chest to help himself breathe. "Oi! That was bad! Not good. Not good. Very not good. Something is wrong. Always wrong!" He leaped up began examining the shelves, closely observing each one. He licked the wood, tasting it. "No. . . no. Nothing here. No sonic. . . hmm. Interesting." He jerked around, a grin on his face. "Now, what's this I'm hearing about missing fillies?"

"What the buck?!" Rainbow Dash exclaimed, looking in confusion at the stallion. "What happened to you?!"

"I don't think you would ever begin to understand, but I'll put it in simple terms-" The Doctor paused. "Stuff." He spun round, going up to Rarity. He looked into her eyes. "Okay, so, what happened to Sweetie Belle?" He glanced at Applejack. "And Applebloom-" Then Dash. "-and Scootaloo?"

"They-wait a second! How do you know their names?!" Applejack asked. "Was Rainbow Dash right? Did you take them? And for the love of Celestia, why were you all wacko and sick a minute ago and now you're all good?! What is goin' on?!"

The Doctor grimaced. "Long story. Would involve lots of talking. Thankfully, if there's one thing I'm good at, it's talking." He nodded, opening his mouth. "But, 'for the love of Celestia', I won't talk. Time to get down to business." The Time Lord hurried out the once again broken door and headed for the TARDIS. He would need her. Unfortunately for him, the six ponies followed. "Yeah, I don't need help, thanks."

"I know you're an alien, and I plan to prove it," Dash said determinedly.

"Great. No wonder you're part of this. Those fillies told you what they know." He kept walking. The pegasus didn't say anything else as the group continued along. They soon arrived at the TARDIS. The Doctor took out his key and opened the door, preparing to slam it in their faces. A blue hoof stopped it and pushed it open on the Doctor. "Don't come in here! Stay out!" He shoved them out and locked the door.

"What are you doing in a box?!" Twilight exclaimed.

"Doing stuff! Bye!" The rising and falling sound of the TARDIS filled the air, and soon the blue box was gone.

Five ponies turned to look at Dash. "Yeah, I told you," the pegasus said simply.

* * *

_**I only have one thing to say**_

_**Ha! GGGGAAAAAAYYY~**_


	4. A Turn for the Worst

The Doctor bit onto his hammer and slammed it down on a panel with a ding. He then flipped a large silver lever, pressed a few buttons here and there, and turned his attention to the little screen floating by his head. The Time Lord groaned loudly. His sonic screwdriver was _still _not done. Only 15% left, though, which was a good thing. He would definitely need it soon.

"Okay, so, three fillies that knew I'm not from here, gone within 24 hours, and now I have six ponies trying to figure me out. Fantastic," the Doctor grumbled, letting his head sink down, eyes dark. "Well, no time to be wasted! Investigation time!" The Time Lord bounced up, and waited until the TARDIS rematerialized and cautiously opened the door a crack. One large, brown eye scanned the landscape from the opening. The exact place he'd landed when he had gotten away from Rainbow Dash. . . the first time. He stepped into the alley and quickly went to the bush the CMC were talking about him in when he had appeared there. He pulled a magnifying glass out from his collar and looked around in the leaves. After a few seconds, he grinned. He slipped the magnifying glass back and found a pair of tweezers instead, using them to delicately pick up the thin pink hair from a leaf. The Doctor pulled his head out from the bush and sprung towards the TARDIS. He sprinted inside to the console and bit onto a nozzle. He gave it a tug. The silvery cord unraveled from somewhere inside the console. The Doctor rummaged under the board of the control panel. When he pulled his hoof back, in it he had a little silver tray and two, very small clips; one red and one blue. The Time Lord attached the tray to the end of the nozzle and then set the light pink hair in it. He then very carefully attached the clips to the hair. He went around to the other side of the controls and pressed a medium sized green button. A slight whirring sound filled the air as the TARDIS picked up the location of the filly's hair. The pink strand lit up for a moment.

The Doctor flashed a glance at it, stretching his neck so he could see. He grinned and then looked up at the blue screen. It turned black. A single white dot appeared in the center. His face fell.

"Oh, not good. Very not good. Blackness. Very dark, wherever those fillies are. And I'm sure that's also very bad for me," the Time Lord commented to himself, grimacing. He shook his head, looking down, and pressed a few square buttons next to him. "Of course, I don't even dare just materializing the TARDIS there." He stopped, his eyebrows furrowed. "But. . . if I flew the TARDIS down there. .?" He rubbed the back of his head, a frown on his face. "Maybe. First I'll have to find where that black is. Darkness, darkness, where would you find darkness. . ." He jerked his head up from where it had been lowered, standing over the controls on his hind legs. "Oh! A cave! A cave! That's it! Alright! Here I go!" The Time Lord yanked a large lever and the TARDIS shifted, groaning. He held onto the console as she rumbled. The Doctor grinned. Always dangerous and exciting, where he went.

* * *

The mouths of five ponies were on the ground. Literally. I mean, seriously, they were on the ground.

Rainbow Dash hovered above them, her arms crossed. A knowing look was on her face as she floated, eyebrows raised. After about five more minutes of silent gaping, she rolled her eyes. "Well? What'd I tell ya?" She nodded firmly. "Alien." Several more minutes of appalled silence later, Twilight Sparkle finally reacted differently. Her mouth opened and closed like a fish's as she pointed at the spot where the TARDIS had once been and then at Dash, then to her and the other ponies. She did that for a few more minutes. Rainbow sighed, face hoofing herself. She lightly kicked Twilight in the back of the head, causing her to finally spit out an answer as she fell forward, landing on her chest with her front legs under her and her rump sticking in the air.

"W-what was that?!" Twilight spluttered, blinking furiously for a few moments. She once again pointed a hoof at the spot where the TARDIS had been. "Can you explain that?! Can _I _explain that?!" She scrambled up, accidently bumping into Fluttershy, who was now laying curled up in the grass in fear. "It just disappeared! It just freakin' disappeared! _That _isn't scientifically possible!"

"I wouldn't say 'impossible'," Rainbow commented, making quotation marks in the air, "as you have magic."

"You-you're saying that was magic?!" Twilight fell onto her haunches.

"No. Just, uh, never mind. Come on, I'll gloat along the way! We need to find that box!"

"Now hold on just one dang minute!" Applejack shouted before the pegasus could fly off. "Ah demand an explanation! We just witnessed an alien, in a box, vanish! Right in front of us! Tell us what that was!" The earth pony stomped her hoof angrily.

"I don't know! All I know is that the Doctor knows what he's doing. He'll know where the fillies could be. I mean, seriously, he made it pretty obvious. We can ask him when we find him. I need to say something though; ha! I was riiigghhhtt! Suck it!" Rainbow did a dance of victory, making sure to end with a hip thrust right at Applejack, who was standing there with a totally not amused face. "Booyah!" She laughed, a smirk on her face. "By the way, the Doctor is as skinny as a twig, like seriously. I swear, he was lighter than Fluttershy."

"So it'll be easy to hog tie 'em and get answers?"

Rainbow Dash smiled evilly. "Yeah." The pegasus developed a more serious tone. "Come on! Let's go!"

"Alright! Alien hunting!" Pinkie Pie cheered as they, although some of them more reluctantly, traveled back into town.

"Seriously?" Applejack deadpanned, looking at the bouncing pony. "You're excited?!"

"Of course! I love meeting new friends!" She smiled so widely she had to close her eyes.

"Even when we're probably goin' to be injurin' him shortly?"

"Yep!"

"Suit yourself."

"I love wearing suits!"

Applejack groaned.

* * *

"What."

The Doctor stood at the entrance to his TARDIS, a confused look on his face. He was not at a cave. In fact, he wasn't even near anywhere that remotely looked like a cave. Or a hole. Or anything of the sort. He was now right in the middle of a grassy field, the sun shining brightly down on him. Small clusters of flowers and wild strawberries were scattered over the landscape. The Doctor fell to the ground, groaning. This was no time for the TARDIS to be recalibrating.

"Come on, old girl! We need to get some work done soon. I can sense something. And you can too. Something's off, just a little fuzzy feeling, barely noticeable," he commented to his ship, standing up and running his hoof down the side of her. He pressed his face against her wooden door, staying like that for a few moments before backing away. The Doctor looked around again, trying to see if he missed something.

No. He hadn't. There was nothing there.

The Doctor went back inside the TARDIS, slowly closing the door behind him. He was going to head back to Ponyville. As much as he didn't want to, he needed to ask around to see if there were any nearby known caves. If the TARDIS didn't go, then he would have to go on foot. He touched down in the alley and stepped outside. A large shaking motion made the Time Lord fall against the blue doors.

A rumbling sound filled the air. Ponies stopped, perplexed and frightened. A scream cut through the air, causing ponies to go wild. They ran around in terror as the sky began turning black. Clouds swirled in the air, uncontrolled by the pegasi who were now being shot out of the sky. They crash landed in buildings and some were even sent hurtling into the EverFree Forest. Lightning crackled in the sky, starting fires randomly.

The towns ponies were now shrieking in horror, running into their homes to hide as the sky darkened. The Doctor stared up at the blackness, his ears flattened against his head.

"This would be it, then. I-owch!" A bolt of lightning struck the TARDIS, sending the Doctor careening across the ground. His violent journey stopped when, albeit painfully, he slammed into a building. The crash triggered another wave of DNA changes.

The Doctor gasped in pain as a burning sensation ripped through his body. His back arching, the Time Lord groaned, pounding his hoof on the ground next to him.

"Ahahaha!" he half laughed, half cried. The Doctor squeezed his eyes shut, a grimace on his face. Taking a deep breath, he managed to roll onto his stomach and look up at the sky.

Dark clouds covered the sky. No rain fell, though something was falling. Medium sized, black creatures shot from the clouds, creating dents as they hit the dirt. They had crooked horns and thin, transparent wings, with a shiny greenish-blueish carapace. They were only about the size of a filly, but had sharp teeth and dark blue eyes with no pupils. Their legs were gnarled, holes covering them. Their short grey manes stuck up in a Mohawk, and their tails were no longer.

The creatures hissed at the ponies left in the streets, the ones that hadn't had enough time to reach their homes. A strange webbing was shot at them, sticking the equines to the ground.

The Doctor tried to sit up, but found he couldn't as another round of searing pain shot through his body. He coughed, lungs refusing to take in air. His twin hearts beat out of control. As darkness crept across his vision, he looked up again.

A large creature, much larger than the others, descended from the heavens. Her blue mane waved in the wind as her translucent wings carried her down. A three-pointed crown was atop her head. Her large horn, misshapen and filled with holes, lit up with a green aura. The clouds shifted and a single beam of light hit her, marking her descent. She landed. Dust flew up in all directions.

"Bow before me, mortals! I am the Queen of the Changelings, and you will all be fed upon by my minions!" she snarled boastfully as she hovered in the air. "Now, my minions, feed! Feed on the love! Spread across Equestria, sparing no one! I shall deal with the Princesses!" The Queen cackled as she prepared to take off. Her drones hissed in delight, immediately attacking the ponies that were stuck in the goo from earlier. Screams of horror rang around the town as the changelings invaded homes and businesses.

"No! Stop right there!" a voice called.

The Doctor looked over with the last of his strength, and saw the six mares standing in front of the Queen. He tried to stand up, but failed.

"We won't let you take over Equestria!" Twilight shouted at the Queen again. She pointed an accusing hoof at the changeling.

"Oh ho ho, really?" the Queen asked smugly. She buzzed over to the group. "And why not?"

"Because we're going to stop you!" Rainbow Dash growled, holding up her hooves in a fighting stance.

"Well, I think not! Your defenders are gone! They're all the way over in the Chrystal Empire!" She laughed.

"How-how did you know that?" Twilight stuttered.

"Seriously, Twilight Sparkle? The changelings have been watching the ponies for a while. Months, now. My minions have reported back to me the status of Equestria and all that's been happening in it. We know all about it, now. You are alone! Cadence and Shining Armor are in the Chrystal Empire, and as we speak, my drones are invading their kingdom, feeding on their love." The Queen hovered over the mane six threateningly. She smirked. "Equestria belongs to me!"

"But you haven't been feeding on any love! You're not strong!" Rarity countered, one eyebrow raised.

"Oh, to the contrary! We have been! We've found a way to feed on love in secret! So, we're stronger than ever!" The Queen threw out her arms. The drones rose into the air, following their leader's command. "Now, devastate this land!" The millions of changelings spread across Equestria, a black cloud covering the sky.

The Queen waved a hoof at the ponies below her. "Toodaloo~"

"No!" Twilight shouted, firing a blast at the teleporting Queen. It missed, and the magenta beam shot off into space. The unicorn stomped her hoof and ground her teeth together. "She got away!" The ponies started yelling at each other randomly.

"Um, you guys, I found something. . . " Pinkie Pie said, motioning with her hoof. The other five looked over at what she was staring at, stopping their arguments. Rainbow Dash flew ahead, her mouth open.

"The Doctor!" the light blue pegasus gaped. She flew down and landed next to him. She furiously waved her hoof for the others to come over there. They hurriedly trotted over.

"Is he. . . alright?" Twilight asked cautiously. The six ponies looked down on him, eyes full of curiosity.

"Fluttershy, analysis?" Applejack inquired like a surgeon.

The yellow pegasus had the back of her hoof on the Doctor's forehead. She pulled it away and glanced up at the others, her face grim. She shook her head. "High temperature, erratic breathing. . . Dash, can you tell me when a minute's up?"

"Sure thing," Rainbow responded. She closed her eyes and focused. Fluttershy put her wing on the Time Lord's neck, looking for a pulse. The time slowly passed. "Done."

Fluttershy sighed. "145."

"What?! How is that possible?!" Twilight exclaimed. "How can one have a heart rate of 145?!" The unicorn shook her head, putting a hoof on her forehead to calm herself. "Alright, alright. What do we do, then? What's happening to him? He's done this twice now."

"I don't know, I've never seen anything like this. Random attacks. . . I don't think it's a heart attack or a stroke, or anything like that. I'm baffled." The timid pegasus shrugged.

"Well, great, just great," Applejack muttered.

"If anything, we should get inside. We're lucky that no changelings have found us, or come for us at all. Come on," Twilight instructed. She lit her horn, which was still smoking slightly from the magic beam earlier, and picked the Doctor's limp body up. "Wow, Dash, you were right, he is really light."

"Can we focus here?" Rainbow Dash asked seriously.

"Right, sorry."

The six ponies rushed to the library and closed themselves inside.

"Okay, everypony, grab your Elements. We need to get to Canterlot and defeat the Queen," Twilight said. She passed the Elements of Harmony out.

"What do we do with him?" Rarity asked, casting a glance down at the unconscious Doctor.

"We leave him here." Twilight lowered her own Element onto her head.

"But what if the changelings find him?" Pinkie Pie asked.

"Oh well. We know what took the fillies now. Isn't it obvious? We find the Queen, demand to know where they are, then use the Elements on her." Twilight prepared to open the door. "Simple as that." The door swung open.

"Twilight, look out!" Fluttershy shouted, pointing outside. The unicorn spun around and was tackled to the floor by a changeling. The breath was knocked out of her. The Element of Magic was flung off, hitting the ground.

It snapped at her neck, trying to kill her. Twilight blasted it off and sent it flying. Dash karate kicked it, and it hit the wall, falling to the floor.

"We're not safe here. Twilight, are you okay?" Applejack asked, helping her friend up. Rarity levitated her crown back to her.

"Thanks, and yeah, I'm okay. That was sudden," Twilight said, out of breath. She put a hoof on her chest to calm down.

"What was sudden?"

Six eyes shot to the pony who had just spoken. The Doctor rubbed the back of his neck awkwardly, looking down. He shifted uncomfortably and kicked the floor as the ponies stared.

"Did. . . did I do something?" he asked.

"What the buck is going on?!" Rainbow Dash exclaimed. She flew up and grabbed the Doctor by his collar, shaking him in the air. "One moment you're laying, knocked out cold on the ground, the next you're completely fine and running around! Tell us, what's happening."

The Doctor, from where he was in the air, looked at the group of ponies. He sighed, closing his eyes. "Alright. I'll tell you. It's going to be complicated, so listen." He paused. "And would you put me down?. . Nicely! Don't want to trigger another episode, do you?"

"I guess not." Dash set the Doctor down. He straightened his tie and cleared his throat. "Start explaining, Doc. We don't have much time." Dash laid back on a hanging shelf, arms behind her head. The five others settled down in a circle.

"So, I'm an alien."

"Yeah, we knew that. What. . . kind?" Rainbow raised an eyebrow.

"I'm a Time Lord."

"A Time Lord? So-"

"You're a Lord of Time?! Awesome!" Pinkie Pie cheered, bouncing up and down. "Does that mean you fix time?"

"Well, kind of, but, I'm not going to go into detail about my species." The Doctor put his hoof on Pinkie's head and pushed her back to the ground. Man that pony was annoying.

"So,_ Time Lord_, what's that box? I mean, seriously, it's a box," Twilight commented.

"That's my ship. She's called the TARDIS. That's 'Time And Relative Dimension In Space'. Best ship in the universe."

"But it's so small!"

"Oi! Don't knock it!" The Doctor gave the unicorn a quick glare. "Anyways, so, you're probably all wondering why I'm here exactly." He started pacing the room. "Well, my ship crashed here. That's when I ran into Dash—literally—and this whole thing began. I could tell right away there was something wrong here. Little fuzzies in energy pulses, things like that. The fillies going missing, I'm guessing that doesn't happen very often. And then this 'Queen Changeling' comes in here with her army. Well, yeah, that's gonna happen when I'm here. Death and destruction follow me, wherever I go. . ." He sighed, rubbing his temples. "So, I'll need to get to my ship. Have an invasion to stop." He turned towards the door.

"Wait a minute. You could take us to Canterlot! We'd get there much faster than walking or taking the train," Rarity said. The other ponies nodded. Their eyes focused on the Doctor.

"I. . fine. Well, come on then! What are we waiting for?" The Time Lord leaped towards the door, taking the lead. "Allons-y!" The seven raced to the TARDIS, getting there without attracting any unwanted attention from nearby changelings. "Here it is! Alright, everybody in!" He unlocked the door and opened it.

"Wait, how are we all going to fit. . in. . there. .?" Twilight's question faded as she entered the spacecraft. The ponys' eyes widened, staring, at the inside of the TARDIS.

"It's bigger on the inside! Now, hurry up, we don't have much time!" The Doctor bustled the six ponies in farther. He closed the door and went to the control panel, beginning to click several buttons.

"Hey, what's this do?" Pinkie Pie asked as she pulled a random lever.

"No!" The Doctor flung himself at the pink pony, but it was too late. The TARDIS shuddered, and the next thing the Time Lord knew he was falling out of the ship. The TARDIS was in flight. He clung onto the bottom of the door step, hoping he didn't fall.

Little harder to grip with hooves.

"Well don't everybody help at once!" he snapped, trying to haul himself inside. Two orange hooves grabbed his brown ones and pulled him in. He jumped up, only to fall over as his legs gave out from under him. He gasped, grimacing in pain. "Q-quick, switch that l-lever off!"

"On it!" Rainbow Dash called, grabbing hold of it and throwing it back into its original position. The TARDIS suddenly stopped, and lowered the fifty or so feet back to the earth.

"H-help me up." He reached up,and the two pegasi in the room flew over to him and held him up. "Take me to the controls, n-now." He was moved painfully over to the console. "Alright, _NO_ more touching stuff, you got that?" He glanced at the ponies, stopping at Pinkie.

The pink pony smiled sheepishly, waving a hoof. "Eh heh, sorry."

"Okay, so-GAAH!" He yowled in pain and the pegasi dropped him in surprise, letting him fall onto the floor. The Doctor winced. "You see that. . . that. . ." He stopped, forgetting what he was about to say.

He couldn't remember anymore.

"That what?" Fluttershy asked, leaning over the stallion.

"I-I. . . I don't recall. . what was I saying again?" He tried lifting his head up but found he couldn't. "And who are you ponies? What are you doing in my. . ." He struggled to find the word, which was getting lost in his mind. "My. . oh, I, what? What's going on? Am I dead or something?" The Time Lord's head pounded. His whole body tensed. Another DNA fluctuation caused him to yell out, the feeling of fire burning in his veins. "AHH-I what? I don't know where I am. . . I think I'm Ten but I don't. . . wait, what's Ten got to do with anything? Is everything always this. . this hard to feel? Because I can't feel my legs. . ." His eyes rolled back in his head, which flopped over to the side, and he passed out.

"Why does this keep happenin'?" Applejack asked, worried.

"He never even said. And what's he talking about? Why didn't he know us? He didn't even know the name of his ship! And something about Ten, I guess, but I'm not sure what that means," Dash commented.

"Well, we don't know how to fly this thing. We've gotta try and wake him up," Rarity said. She reached out her hoof and shook his shoulder, jostling him.

"Here, let's try this." Rainbow shouted at the top of her lungs, causing the others to wince and cover their ears. Pinkie tried her handy-dandy flugelhorn, which didn't work either. Twilight summoned a bucket of water to douse him with, but all that did was make him let out a violent yell and thrash about a bit. Applejack pulled his eyelids up and looked at his eyes.

"Well, this ain't workin'," the southern mare said, announcing their thoughts out loud.

"Shoot. What're we going to do now?" Dash asked.

"We're going to go to Canterlot, remember? You know, defeat the Queen?" the Doctor reminded them, having just opened his eyes.

"What!? How-!? Okay, tell us what's happening to you! We need to know," Twilight demanded.

"Isn't it simple? I'm not supposed to_ be_ a pony. I changed. My DNA's now trying to fix everything, and it's slowly making me forget who I am. It's going to change me permanently into a pony, and I'll be gone. Boom. No more Doctor. So, if you'd please stop getting me thrown out my own ship, or kicking me into a bookshelf, or tossing me in the air, that'd be great. I don't have much longer until the full transformation, so we need to get this over with," the Time Lord told them. He stood up and got the TARDIS on its way. The wheezing of the engines announced their arrival as the materialized in Canterlot Castle. "Okay, let's turn this thing invisible. Don't want any changeling getting involved here." He flipped a switch and the cloaking device turned on. "Stay in here while I quickly check it out." He poked his head out.

"I thought Cadence and Shining Armor sent you packing last time we met, Chrysalis," a tall white alicorn commented sourly from where she was stuck in green goo.

"Oh, but we unpacked here in Equestria, setting up base. There's no stopping us now, Celestia," Chrysalis gloated. She paced the throne room, smirking.

"Release us, foul mare!" another midnight blue alicorn snarled from across the room, where she too was enveloped in the sticky green goo. "We shall smite thee!" She flapped her wings, which were free from the goop, trying to escape and tackle the Queen.

"Oh, please, Luna, all that formal talk is really getting quite irritating." The changeling flew around the younger alicorn. "I would stop talking if I were, less anything happen to your sister. ."

"Leave her alone!" Celestia growled, struggling in her bonds.

"Silence! No more talking for either of you!" Chrysalis shouted, sending a wave of energy across the room. The two sisters cried out as they were hit with the magic, not talking anymore. "I go to see how my minions are faring." She hovered out of the room.

_Ding!_

The Doctor flashed a glance at the screen as he closed the door. His sonic screwdriver was done! He went up to the console and grabbed the probe out of its slot.

"Alright! Sonic screwdriver!" he cheered, flipping it in his hoof.

"What's that thing?" Rarity asked, pointing at it.

"My sonic screwdriver. I'll explain more later."

The Doctor motioned to the ponies to stay there. He crept out, keeping low behind the throne. The TARDIS had landed right next to it, but thankfully the Queen had been too focused on the Princesses to notice the sound of the engines or the ship itself.

The ponies in the TARDIS were waiting, anxious to know what was happening. Meanwhile, Twilight was inspecting the controls. She reached the screen, tapping it. It flickered on, and she saw what was happening outside.

"Hey! Look at this!" Twilight hissed, waving her hoof. The five mares scurried over and watched silently.

The Doctor reached Celestia, who was trapped on the other side of the throne.

"Who are you?" the Princess asked, baffled, as the Doctor broke the strands of goo sticking the ruler of Equestria.

"I'm the Doctor. Now sh!" he silenced, and Celestia fell quiet. He continued breaking the strands. He didn't notice that the Queen of the changelings was entering again.

"Now, what do we have here?" she asked slyly, standing at the entrance of the room.

The Doctor spun around, ears flattening against his head. "Oh! My, I didn't notice you coming in. Hello!" He backed away slowly, back towards the TARDIS. Chrysalis stalked towards him.

"Freeing my prisoners? Naughty, naughty, naughty!" She licked her lips, horn glowing.

"I, um, I should be leaving! I-"

Smack!

The Doctor turned around just as he ran into the TARDIS. He fell over.

"Quick! Grab him!" Twilight hissed. Rainbow Dash quickly opened the door and tugged the Time Lord inside before a bolt of green magic slammed right into him.

Outside, the Queen raged. "That's it! These games, Celestia, they will end! Time for my secret weapon!"

The whole country was hit with what seemed like a giant earthquake. Buildings crumbled. The earth cracked, giant splits running across the ground.

The Princesses screamed as Chrysalis laughed, her cackling filling the air.


	5. Well guess who fucking died now jesus

The ponies were flung around the TARDIS, which was was falling. Rainbow Dash clung to the Doctor, who had fallen back into his coma-like state. Fluttershy and Rainbow Dash hovered in the air, dodging bits and pieces of the spacecraft and just other random bits of junk the Doctor had left laying around.

The shifting stopped, allowing the ponies to get their breath back.

"This is just like when Discord turned my house upside down!" Fluttershy squeaked in terror, her eyes watering. "Oh goodness! He was here! He was here when the Queen took over!" Her hooves went straight to her face in horrific realization. "She probably did something to him! We have to save him!" Fluttershy waved her arms in the air frantically. Her eyes then rolled back in her head and she fell out of the air.

Rainbow Dash, balancing the Doctor in one arm, reached forward to catch the unconscious pegasus as she went limp. "Well, just great. We have two knocked out ponies on our hooves, but this time one's an alien and in a coma." The pegasus rolled her eyes. She moved to the right as a wire came loose, ending up slamming into Rarity.

"Ooh! This is simply horrid!" the unicorn complained as she rubbed her side. Rarity suddenly fell forward, landing on Applejack. The earth pony gave a cry of surprise as the TARDIS flipped upside down and shook. Pinkie Pie was sent flying over the three ponies on the ground, a springing sound coming from where she landed. The lights in the TARDIS flickered, the room being pitched into darkness for a few moments.

"I agree!" Twilight Sparkle shrieked, hanging onto the railing of the ship as her eyes went in all directions, the shaking increasing. She curled up in a ball when a hammer pounded her in the flank. "Somepony do something!" She lost her grip and fell into a pile of junk. The TARDIS gave a final screeching sound, a violent jerk, and then all was calm.

"Okay, Ah think it's over," Applejack breathed, standing shakily up. The earth pony helped a slightly bloody Rarity get to her hooves by holding her friend under the arms with one of her own wrapped around her waist.

"Everypony okay?" Twilight called from where she poked her purple head out of a life saver.

"I'm okay!" Pinkie announced. Everypony's eyes went to where the pony was hanging, wires tangled around her back legs and up to her midsection. She let her arms dangle as her fluffy mane fell into her face.

"Ah'm good!" AJ answered.

"We're all fine. . . I think. Rares, you alright?" Rainbow Dash asked, looking at the white unicorn leaning on Applejack's back.

Rarity tried giving a weak smile, but ended up cringing instead. "I, well, mostly. A cut, really," Rarity coughed.

"Here, let me look," Twilight said. She pulled her head from the life saver and smoothed her indigo mane before trotting over to Rarity. The purple unicorn inspected the injury, which was on Rarity's flank. A long, shallow cut stretched from the lower diamonds on her cutie mark to the bottom of her flank. "Not too bad. . but not good. AJ, can you see if there's a first aid kit anywhere in here? He must have something." She glanced at the earth pony, who nodded and went off to search the console and the assorted junk. "And Rainbow Dash, will you please get Pinkie down?"

"I'm on it!" Dash shouted. She carefully set the two passed out ponies in her arms down on the chair next to the railing. Then the blue pegasus flew up and started helping Pinkie Pie get untangled.

Turning to Rarity once again, Twilight asked, "does it hurt?"

"Seeing as how there's a gash on my leg, YES!" Rarity shouted, shoving her face in the other unicorn's. Twilight crinkled her nose before pulling away.

". . Right." Twilight looked at Applejack. "Any luck?"

"Ah can't seem to find anythin'. Ah'll keep lookin' though! Just give me a minute. ." the earth pony trailed off, bending over to rummage through a chest. She kept one hoof on the edge of it as her upper body and head disappeared. "This thing's huge! It's so much. . ."

"Bigger on the inside?" Pinkie Pie decided to finish for her, still hanging upside down from the wires constricting her.

"Yeah. Exactly." AJ brought herself back to her full height. "Nothin' in there, though."

"How about around the controls or something?" Rainbow Dash suggested, taking a wire in her mouth and tugging at it.

"Ah'll take a look." Applejack trotted over to the console and looked under it. "Oh hey, there's stuff under here!" AJ looked down under the paneling. She looked up at Twilight. "Would ya do me the honors?"

Twilight smirked. "Of course. It'd be my pleasure." She lit her horn, lifting the panel up so Applejack could get under it. The earth pony reached her head in and reemerged with a first aid kit held in between her teeth. Twilight took it and started cleaning Rarity's injury.

"Ow! That burns!" the unicorn complained as Twilight dabbed at it with some alcohol on a fabric pad. She rolled her violet eyes as Rarity huffed dramatically. She yanked her leg out of the way, holding it close to her body.

The purple mare fell forward, as she had been leaning in and Rarity pulling away had caused her concentration to fail. Twilight's head popped up, first aid kit on her head. She pointed a hoof at Rarity accusingly. "You need to hold still! I can't have you wiggling all over!"

"I am_ not_ 'wiggling'! I simply, how may I put it, _repositioned_ my leg to a more comfortable pose." Rarity watched as her fellow unicorn got to her hooves.

"Just don't, will you?" Twilight shook the kit off her head.

"Fine. Just be more careful." Rarity turned away.

"But, but-"

"No point, Twi," Dash intervened, fiddling with a dark blue wire wrapped around Pinkie's hind leg, not even turning to look at the unicorns.

Sighing, Twilight continued to clean and dress the wound. A bandage was wrapped neatly around Rarity's flank and leg.

"Thanks, Twilight. Feels much better," Rarity said, carefully putting weight on her leg.

"Almost done up there?" Applejack asked, turning her face up to look at the hanging pink pony and the blue pegasus.

Rainbow Dash grunted, a different black wire in her mouth. She dropped it once she had gotten Pinkie unraveled. "Almost." She yanked a silver wire from around her friend's rump and the party pony slipped loose of the other remaining wires, dropping to the floor like a ton of bricks. Dash dusted herself off, a cocky smile on her face. "All done." She hovered to the floor and folded her wings.

"Okay, now what?" Rarity asked. She raised a hoof in question.

"I say we go see what's going on. There was just this, like, giant earthquake! Something happened," Twilight said.

"Thanks, Captain Obvious," Rainbow put in sarcastically, snorting. Applejack shot a glare at her, which the pegasus promptly ignored.

"I can't say I'm excited about this," Pinkie Pie told them after standing up.

"Let's check out the thing again," Rarity suggested. "The little screen." She pointed at the console, where the screen was attached, broken images of Gallifreyan spread across it.

"Good idea," Twilight agreed. The ponies gathered around as Twilight tried to get it working again. The screen flickered momentarily before switching to the camera.

"W-what was that?!" Celestia demanded, struggling in the slimy green goo. Dust from the ceiling rained down on them, making the Princesses cough.

Cracks ran through the walls and floor, making the whole room seem like a valley. The throne had been dislodged, laying on its side, destroyed. The stained glass windows were shattered, shards of the brightly colored glass laying scattered over the throne room.

In all, it seemed like the whole castle had fallen.

"We demand thou tell us!" Luna added, wings pumping.

Chrysalis smirked, flitting across the absolutely ruined throne room. She came up to Celestia and stroked her face, to which the alicorn drew back from, her face contorted into one of extreme anger and fear. "Oh, wouldn't you like to know?" The Queen laughed. "Well, you'll see. And I think you'll be surprised." Chrysalis stepped away from Celestia.

"You see," she started, "we've been planning this for a while. Discretely feeding on love, plotting. Ever since we were first defeated.

"But even though we've taken over Equestria, I'm afraid it still isn't enough to satisfy our massive army's needs."

"What do you mean 'we'?" Celestia demanded, half angry and half confused.

"Hold on, hold on, I'm getting to that part," Chrysalis said, waving her hoof. She leaned in close to the Sun Princess's ear. "It's the best part."

"Anyways, our army has grown. We are stronger, yes, but not strong enough. We need more love. Millions of changelings is too much for even Equestria.

"So I devised a plan.

"And now, with the help of them, we will conquer the whole world!" Chrysalis threw her arms in the air, hovering a few inches off the cracked floor. She then called out. "You can come out now, my sweets."

The Princesses held their breaths. The ponies inside the TARDIS held theirs, too.

It seemed like the entire world just stopped, waiting.

Three figures emerged. They were the same size of the Queen, but were not her. They were obviously female.

The first one, white, with a shiny purple carapace that faded into pink, was a unicorn. Or what looked like a unicorn, at least. It might be a bit generous to call it even unicorn-like. Her large, crooked horn was surrounded by curly light pink and purple hair, filled with holes, and so was her swirly tail. Large green, slitted eyes shone in the darkness.

The second, an earth-like pony, was pale yellow. Her carapace was red that faded into sunset pink. Her mane was dark pinkish red, and flopped over her head. Her tail curled around, and like her mane, was filled with holes. Sunset pink and orange eyes, like a cat's, stared at the Princesses, unblinking.

The last, pegasus-like, was orange. Her carapace was purple that faded into blue. Her large, translucent wings were positioned upright on her back, much like an insect's, and were shaped as such. A slightly curly purple mane with a Mohawk going down her neck, and a matching tail, were adorned with holes.  
Lavender slitted eyes peered out at the others in the room.

They all had sharp fangs, along with the hole filled, lanky, twisted legs. They were also all the same height. The three blinked at the same time, slowly.

"What. . is this? What have you done to them? I recognize those fillies! They were at the Royal Wedding! I've seen them several times!" Celestia shouted in horror.

"Is that. .?" Rainbow Dash started, her words lost in her throat as she lifted a hoof up to the screen. The colors and features of the three changelings made it easy to identify them.

"Ah-Ah can't believe this. . That stupid bitch murdered my sister and made her into a changeling!" Applejack screamed, tears already forming in her emerald green eyes.

"Applejack, wait!" Twilight shouted, reaching out a hoof to stop the orange mare from running out the TARDIS doors.

"Ah'm gonna buckin' kill her!"

Before the earth pony could get out, Dash had shot up and tackled her, holding her to the floor, kicking and screaming.

"AJ! Calm down!" the pegasus ordered, putting one hoof on Applejack's neck and another in the center of her back.

"Sweetie Belle! Oh my precious sister!" Rarity bawled, dropping to the floor, tears streaming out of her sapphire blue eyes. "Of all the worst things that could happen, this is THE. WORST. POSSIBLE. THING!"

Pinkie Pie patted the sobbing unicorn on the back, trying desperately to console her.

"Oh calm down, all of you! They're not dead!"

All eyes went to the Doctor, who was laying on his back on the small chair, with Fluttershy on top of him.

"They're-they're not?" Applejack stopped struggling and hopefully perked an ear. Rarity lifted her head up and Rainbow glanced over her shoulder.

"No, of course not! And-"

"Why was I asleep on top of the Doctor? Oh no, we didn't do anything did we? I'm-" Fluttershy didn't get to finish her sentence as the Time Lord shoved his hoof in her mouth.

"No, we didn't. Now, if you'd please. .?"

Fluttershy gave a flap of her wings and managed to lift herself off the stallion. She hid behind her hair, blushing slightly.

"Anyways," the Doctor started, "as I said, they're not dead. Just, well, different. I think we'll be able to change them back afterwards. But right now, we have to stop Chrysalis. Any objections?"

Six head shakes, along with one blue pegasus snarling, punching a hoof into her other one.

"Alright then! Allons-y!" The seven rushed forward, only to crash into each other in a domino effect as the Doctor stopped in his tracks. "Um, actually, you six wait here. I need to do something."

"Um, can I ask you something real quick while we're stopped?" Fluttershy asked quietly. Every head turned to look at the timid pegasus. "I-I. ." She looked down, scraping a hoof along the floor. "We should find Discord. He, um,_ is_ the God of Chaos. He could help us, plus, I couldn't stand to think about if he was hurt!" Fluttershy started crying, large blue-green eyes filling with tears. She put a hoof over her mouth to stifle the sobs, but everypony could still hear them loud and clear. Pinkie Pie let the pegasus cry into her shoulder.

"Right! Doctor, Discord could definitely help us. His magic defies every law of physic and science there is. He's the most powerful being in the land, only outmatched by the Elements of Harmony," Twilight added. She suddenly stopped. She reached up felt her head. "My Element! And yours! They're gone!" The other five mares looked at their chests.

The Elements were, as Twilight said, no where to be seen.

"Where could they have gone?!" Applejack exclaimed, eyes wide.

"We must have lost them when the earthquake thing happened. I'm sure they're here somewhere," Rainbow Dash added.

"We have to find them!" Twilight shouted.

"I'm sorry girls, but we don't have to look for those. They're not going to work," the Doctor said.

"Yes they will! The Elements of Harmony are the strongest magic known to ponydom!"

"They won't."

"And how do _you_ know that? You've never even seen the Elements working." Twilight glared at the Time Lord.

"I read up on them. Trust me, I know. I can't explain now, lives are in danger." The Doctor looked at Fluttershy. "Where would Discord be, do you think?"

"Well. . I don't really know. He just usually goes where he wants to. All I know is that he was at the castle when Chrysalis's drones started attacking," Fluttershy told him. Her eyes were big and watery.

"Okay, hmm. . Guess we'll just have to start looking. Let's move this box!" The Doctor grinned foolishly and sprang up to the controls, slamming a hoof down on a button. A showering of sparks rained down upon the ponies, making Fluttershy squeak and hide behind Dash's legs for cover as she cowered. ". . I guess not then. We'll have to get out of here somehow, and just simply walking out like, 'hey, Chryssi, what's up? Oh nothing, just going searching for the God of Chaos'."

"I could. . . teleport us out?" Twilight squeaked, her voice raising an octave.

"Well, why didn't you say that earlier! Come on! We don't have much time!" the Doctor shouted, putting his hooves on Twilight's chest.

"Get off!" She shoved the Time Lord away angrily, huffing. She then swallowed nervously. "O-okay, here I go. I'm not sure if this will work. . ." Her horn lit up, magenta magic spreading across the room. It gripped at the ponies, and suddenly her horn flashed. Pain seared through the bodies of the ponies as they were teleported out of the TARDIS and into an abandoned room of the wrecked castle. Twilight wobbled uncertainly on her hooves, barely managing to stay upright. The others coughed, the odd sensation of being moved from place to another freaking weird.

"Okay, man, that was. . . intense. Right! Let's go!" the Doctor cheered, and set off. A crippling pain shot through his chest before he could get the door open. He cried out as his hearts pulled at each other. They were trying to merge into one.

"Gah! No! Lefty, stay with me!" He pounded on his chest, trying to stop the heart from failing.

"What's happening? Is it doing it again?" Pinkie Pie asked. She looked around at the other mares.

"One of my hearts isn't working!" the Time Lord choked out, falling to the floor.

"Wait, _one_?! You have more than one heart?!" Twilight exclaimed in disbelief.

"Yes! Now, someone help me!"

"A-alright!" Rainbow Dash flew over and stood in front of the Doctor.

"Hit my chest!"

Dash pulled her hoof back.

"Left side!" the Doctor cried out before she could pound him. A blue hoof struck him on the left side of his chest, causing the Time Lord to grunt in pain. "Again!" Another punch in the chest.

"Wait, wait! I got it!" Twilight shouted. Her horn started burning, a blinding light filling the room. "It's a spell I learned! It can start somepony's heart!" The unicorn squinted from the sheer brightness of the spell, and her friends shielded their eyes with their arms.

"Whoa, Twilight, that-"

A bright beam shot out, right into the Doctor's chest. Rainbow Dash sprang out of the way before it could hit her too. The breath was knocked out of the Time Lord as it pinned him against the marble doors behind him.

As fast as it had come, the beam winked out, leaving Twilight's horn sizzling. She carefully dabbed at it with her hoof, looking up at the burning bone.

"Doctor? Are you alright?" Rainbow Dash waved a hoof in front of the Time Lord's eyes as he stared off into space. He jolted from his trance, seemingly surprised at the pegasus's presence.

"Wow! What a spell! Enough time wasted already. Allons-y!" They were off again.

The seven searched through rooms, fighting off whatever changelings they found and kicking the flanks off them.

"Um, have any of you guys looked out the windows, well, what's left of the windows yet?" Pinkie Pie asked, her worried voice coming from a spare room across the hall. Six other ponies arrived in the room and looked out the broken windows.

Equestria was in total destruction. Houses were burning, giant splits in the earth running across the country. The bodies of ponies lay scattered along the streets. From what they could see, nothing was good.

Ponyville in the distance, along with other towns and cities, fared no better than Canterlot.

"Have you looked _down_?" Applejack asked, dry mouthed. The Canterlot Castle was demolished, bottom floors crushed beneath the top floors. The gardens were no more, just trampled bushes and powdered statues.

"Oh my," Rarity breathed, the carnage horrible to behold.

"The sky is so. . black," Fluttershy whispered, cowering beneath Rainbow's belly.

"This is horrible," Twilight murmured. Millions of changeling drones buzzed through the skies, searching for more victims and patrolling the Canterlot Castle, in case any moron decided to stand up to the Queen.

"We need to find Discord," the Doctor announced solemnly, face dark. He turned away from the window and went into the halls again to look through more rooms.

The search continued, all the way to the bottom floors. Eventually, they found what they were looking for.

Applejack pushed the broken door open further, its hinges so loose that once she did move it, the door clattered to the floor. The earth pony winced, folding an ear back, and stepped over the fallen door. Her green eyes glanced around the room warily. They eventually stopped on the still figure laying on the carpet in the center of the room, back to her. AJ froze, her breathing shallow.

"F-Fluttershy! Ah think Ah found 'em," Applejack called softly. The timid pegasus stopped in her search and poked her head around the doorway. Her eyes lit up immediately.

"Oh, Discord! I-" She stopped, pupils growing tiny. The limp figure on the ground didn't move at all. Not even once. "D-Discord?" Fluttershy took a small, almost nonexistent step forward.

"Ah'll go get the others," Applejack said, the words barely heard by the pegasus's ears.

Fluttershy stood frozen in the doorway, heart pounding. She began moving forward, inch by inch, and she soon found herself by the spirit's side. Her breathing labored, Fluttershy put a hoof on Discord's shoulder.

Ice cold.

Fluttershy's eyes teared up immediately, her heart skipping a beat. Fear made her remove her hoof from his body and set it back down at her side.

"Discord, please. . please get up," Fluttershy pleaded quietly, dropping to the floor. She gasped as her belly fur was soaked at once. She looked at the carpet, which was red. She hadn't noticed all the blood, as the carpet was the same color.

"Fluttershy! We heard that Discord was-" Twilight stopped as she saw the heart broken pegasus stooped by the spirit's still form, her stomach covered in a red substance. Fluttershy kept her eyes locked on Discord for a few more moments before slowly turning to look at the five ponies in the doorway. Tears ran down her face, eyes screaming 'why'. Her face was frozen in a looks of absolute horror and disbelief. "Fluttershy?"

"Is he. .?" Pinkie Pie asked, voice high. Rarity locked eyes with the party pony, nodding slowly. Pinkie gaped in disbelief as she let Rarity hold her, tears falling down their faces.

"Ah'm sorry, sugarcube," Applejack whispered, hat held to her chest.

As the group fell into a lapse of silence, the Doctor finally got to the room they were at. He walked in, and knowing immediately what had happened, went up to the silently crying pegasus in the center of the room.

"I'm sorry. I'm so sorry," he said, standing right beside her.

"But-but. . he had just realized that having friends is good. He finally had a friend, and I let him down. I wasn't there for him," Fluttershy whispered, her voice no more than a breath. Tears rolled down her face in copious amounts, the true horror of the situation taking hold of the little pegasus.

"T-Twilight, can't you do that spell, the one that starts somepony's heart?" Rainbow Dash asked, hovering above the group with her arms crossed.

"It only works if the pony was in fairly good health when they died, and it would've had to be right afterwards. It only works for about three minutes after death, at the most. And besides, it takes too much energy to do it twice in one day," Twilight responded sadly, blinking slowly as she watched their friend cry in front of Discord's limp body.

The Doctor watched this all go on. His face was dark, yet devoid of emotion. But he was in inner turmoil.

What should he do?

Yet, he knew what he should do. Even if it wasn't the wisest thing to do.

The Doctor closed his eyes, and opened his mouth. A steady stream of regeneration energy poured out of his body and into the still God of Chaos.

The ponies watched, eyes filled with tears, as the energy dissolved into Discord. Fluttershy was about to ask about it when Discord's back suddenly arched, and his eyes snapped open. He drew in a long, deep breath before falling back onto the bloody carpet.

"DISCORD!" Fluttershy screamed, voice pitched up an octave, as she stood before the spirit.

"Quick, I only gave him life, he'll die again if his injuries aren't tended to," the Doctor intervened before she could get too carried away. The next hour was filled with cries of agony and happy sobbing, (mostly from Fluttershy), as Discord's wounds were cleaned and bandaged. As the sprit was partially awake the whole time this was going on, it wasn't a very pleasant time for him.

Discord, all in all, was in pretty bad shape. One of his wings was broken, and a few ribs were, too. Something sharp had obviously tried to cut him in half, as the three hundred stitches to seal the wound showed. That was the worst injury, the one that had made him bleed out on the carpet in the end. His deer antler was snapped off also. Cuts and bruises were scattered all over him, plus a black eye was an addition to the collection.

"What. . what happened?" Discord mumbled, still half asleep. Fluttershy stroked his nose gently, a sad smile on her face.

"Sshh. . . you need to rest. You're in pretty bad shape, sweetie," Fluttershy said softly. She sat next to him, content as he passed out.

"What did you do? You. . saved him," Rainbow Dash said, voicing their thoughts.

"Well, I just might've used the _teeniest_ bit of regeneration energy to save him. I've seen too many people, and, um, ponies. . . or even weird dragon-pony things die today to let him just lay there in a pool of blood," the Doctor said, giving them a small smile.

"Thank you. Thank you so much," Fluttershy said as she snuggled against Discord further.

"You're welcome. Now, we better get back to the TARDIS. We still haven't figured out our problem about what to do with this whole changeling situation."

* * *

"So, my sweets, you feed on the Princesses while I go and take a nap. All this destruction sure makes one tired," Chrysalis told the changelings, yawning with a hole-filled hoof up to her mouth to stifle it.

"Yes-" Sweetie Belle agreed, voice monotonous.

"We will-" Apple Bloom added.

"Feed on the Princesses," Scootaloo finished.

Chrysalis purred in delight. "Good. Now, I'll be off." She exited the room, door closing behind her.

"Stop this at once! I know you might be confused but you are not changelings! You are three, sweet little fillies who would never hurt a fly!" Celestia shouted as the transformed mares walked in sync towards the bound Princess.

"Stop, we commandeth thou!" Luna snarled, wings once again flapping.

"We-"

"Will not-"

"Stop," they said, talking in the same monotonous voices and order every time.

"We were-"

"Born-"

"To kill."

"No! You were not!" Celestia argued, trying to get the once-fillies to remember who they were.

"She's right, you know," the Doctor said, voice plain. Five heads turned to look at him; three full of hate, and two full of shock and hope. "You weren't born to kill. You were born to live." He raised an eyebrow as the changelings hissed together.

"And who-"

"Just exactly-"

"Are you?"

The Time Lord gasped, feigning shock as he put a hoof to his hearts. "You really don't remember me? The mad man with a blue box? How strange. . " The Doctor jumped up on a cracked windowsill, kicking a clump of fallen marble.

"We demand-"

"To have-"

"An answer!"

"Oh, do you now?" he asked, looking up. He shrugged. "Nah, I don't think I'll tell you. And you know what? You remind me a lot of the Daleks. They're a lot like you; monotonous voice, demanding nature, no emotions-but hate-and you take your orders from another. You are soldiers; designed to receive orders." He clicked his tongue, his eyebrows raised. The changelings stayed still. "You wanna know what they called me in the ancient homeland of the Daleks?"

A pause.

"The Oncoming Storm." The Doctor grinned evilly. "And, oh, one more thing-

"I read up a little on changelings while at the library. And I know they have really sensitive ears~" The Time Lord pulled his sonic screwdriver from his collar when he said that, and the ponies inside the police box flipped a switch, sending sound frequencies so high at the changelings that they toppled to the ground, shrieking and clawing at their ears in desperate attempts to block the sound. The Doctor cringed slightly and saw the Princesses do the same. He ran over and took a squirt bottle form his collar, spraying a liquid onto the goo restraining Celestia. She broke free as the goop dissolved almost at once.

"How did you do that?" the Sun Princess asked, astonished.

"You really think I would've left without getting a sample of what I'm dealing with?" The Doctor snorted and raced over to Luna, doing the same to her. She gave a hard flap of her wings and soared over the two ponies. "Okay, follow me!" The TARDIS became visible and he threw open the doors.

"We're getting inside a box?!" Celestia exclaimed.

"Now, with all due respect, GET IN THE BOX!"

Luna shrugged and then pulled her sister into the spacecraft, with the Doctor entering behind them, doors slamming shut.

* * *

_**Yeah. . . there's a reason this ain't for kiddies.**_

_***stupid ass laugh***_


	6. Oh, you think you've won?

_**Yeah, yeah, I got burned. Some of you people. . . *sigh* Anyways, I'm explaining some things! (Discord dying). And adding more confusion that will be solved in either this story or the sequels! And don't worry, the fun isn't over yet! *wink wink***_

* * *

Princess Celestia and Luna looked at their surroundings, eyes wide, mouths open. The Doctor rushed by the two, and to the console. He put the lever back into its former position.

"I have to do some work, so if you'd move, your highnesses?" he asked, bowing slightly. He motioned to the panel they were standing on. The Princesses, still shocked, moved stiffly back. The Doctor grinned. "Thanks!" He grabbed his tool and pulled the panel up, then wiggled himself under it, going to the controls underneath. He laid on his back and started fixing some broken wires. He got out his sonic screwdriver and fused them back together.

"What. . . is this place?" Luna finally asked.

The Time Lord grunted, putting a hoof up and motioning towards some screws on the top of the console. Rarity saw and picked them up, setting them in his extended hoof.

"Does thou hear us?" Luna repeated. "We demandeth to know where we are!"

"Luna," Celestia said, laying a hoof on her sister's shoulder.

"Sorry. Old ways of speaking are still stuck in my mind." The Princess of the Night shifted slightly. "I still demand to know where we are!" She rested her aqua gaze on the Doctor.

The Time Lord glanced up momentarily. He raised an eyebrow, taking the sonic screwdriver out of his mouth. "You're in the TARDIS, of course! The best ship in the universe! Now, if you'll shut up, I'll just get back to getting us out of here." He focused on the console again.

"How rude! You do not speak to us that way!" Luna shouted, volume rising.

"Princess, if you'll just calm down. ." Twilight Sparkle started warily. She approached the alicorn. "It's really complicated and I still don't even understand."

"Fine. But I demand a better answer later."

"Twilight, my most faithful student, I'm so glad you're alright," Celestia said. She bent down to give the unicorn a hug. "I was afraid you'd been hurt."

"No, I'm fine. I was worried about you," Twilight replied. Her eyes widened suddenly. "Oh, no, Spike! I don't know where Spike is! Oh my gosh, I'm such a horrible pony! I didn't even think of him!" She started panicking, until a large white wing was draped over her back. The tearful mare looked up at her mentor.

"I'm sure he is fine, Twilight. We will find him."

"Unless Chrysalis did to him what she did to Discord," the Doctor put in, shining his sonic on a wire.

"What do you mean? What happened to Discord?" Celestia asked, her voice wavering.

"And what do you mean Chrysalis?" Twilight asked, confused.

The Doctor sat up, only to hit his head on the edge sticking out on the console. He winced, rubbing at the spot. He then carefully sat up and hopped out of the area, setting the panel down into its original position.

"Isn't it obvious? Discord, as you ponies described, is the most powerful being in the world. He can do anything; defy every law. So, why would he be killed when everyone else is just being attacked?" the Time Lord said.

"What?! Discord is d. . dead?" Luna gasped, ears falling to the sides of her head.

"No, no. But he was. Anyways, since Discord is so powerful, it's only fair that Chrysalis would go after him. She killed him, not wanting to risk him defeating her, thus ruining her plan."

"But how did Discord die anyways? Aren't the Princesses and Discord immortal?" Rainbow Dash asked, putting her hooves up in question.

"In a way, but it's no immortality. It's just a never ending life. Their lives never end, they just keep going on, forever and ever."

"Like yours?" Pinkie Pie asked.

The Doctor froze. ". . Yeah, kinda like mine. But, not quite." He cleared his throat. "Again, back to the point. So, with Discord out of the way, Chrysalis would have nothing to stop her. She'd already had a plan for the what to do with the Princesses. She would disguise as them, and feed on their love for each other, and the never ending love from their subjects. For what's more powerful than love from a sister who's been away for a thousand years?" He saw the looks in the sister's eyes as he finished; the horror and the sorrow, the regret and the pain, anger and hatred.

"And there's another reason Chrysalis killed Discord: he didn't love. He did _not_ love. He hated, he despised others for their perfection. He would serve no purpose to her. She could not control his chaotic magic, so strong that even he did not have total control over it. Some things, sure, but it's chaos.

"After all, what is chaos? No control, no order, total disharmony. The most powerful magic of all, in the hands of one lonely draconequus who was alone in the world and surrounded by creatures who called him a monster. There was no way he could love. Not in a million years.

"So she killed him."

The eight ponies stayed still. The Doctor turned around and began pressing buttons of the console. The room seemed darker.

"But Discord is reformed! He started loving! He. . he. . I love him," Fluttershy stammered, eyes filling with tears. She hid behind her mane, which covered most of her face.

"Yeah, Flutters's got a point!" Rainbow Dash agreed.

"Well-"

The Doctor didn't get to finish as the TARDIS was hit with something. The ponies cried out as the flopped on top of each other. The lights flickered, sending out sparks.

"Can't your box ever stay still?!" Rarity exclaimed. She cringed as Pinkie Pie's back hoof accidentally kicked her injured leg.

"It's not the TARDIS's fault! Well, not this time. ." the Doctor mumbled from where he was crushed under Celestia and Applejack. He squeezed himself out just enough to where he could pull the lever to make the TARDIS move. He fell back to the floor, stretched to his limit.

The sound of the TARDIS engines filled the air.

"Aw, music to my ears!" the Time Lord sighed from beneath the ponies. "Now, move your rumps!" He stopped. "Oh, I'm being rude again aren't I? Sorry."

"Yes, ya are, and it would be my pleasure," Applejack huffed as she clambered off the Doctor's back. Celestia hauled herself off as well and brushed some dust off her shoulder, taking the time to readjust her crown.

Pinkie pulled away from Twilight as Rarity got shakily up to her hooves. Rainbow Dash and Fluttershy were still hovering in the air, as the crash hadn't affected them. Luna stood up from across the control room, her crown knocked off. Pinkie Pie found it tossed it over to her, much to the Princess's pleasure.

"I'm guessing that bang was the changelings trying to get in," the Doctor mused.

"We should probably keep them away. This is only wood, after all. I'm surprised it even survived the castle falling apart," Celestia mentioned.

"Oh please! This box has got extrapolator shielding; almost nothing can get through." He knocked on the wall with a hoof.

"Almost nothing? Does that exclude changelings or not?" Twilight asked.

"I very much doubt magic will be able to destroy the TARDIS," the Time Lord snorted disbelievingly.

"Alright then."

"Now, let's see where we are, shall we?" He approached the doors. But before he could, a beam of blue magic shot at him from behind. The Doctor gasped. His eyes rolled back in his head as the magic worked. It released him and he fell to the floor.

Every pair of eyes went to the Night Princess, whose horn was still glowing slightly. Her eyes were closed.

"Luna! What did you do?!" Celestia shouted, appalled. Her sister's aqua eyes shot open, glowing briefly for a moment. She looked at the Doctor, who was still laying on the floor.

"He's not one of us," Luna said blankly. She furrowed her eyebrows. "He's not one of our kind."

"Well, he is an earth pony."

"No! That's. . that's not what I mean." Luna locked eyes with her sister. "He is not a pony!" She stomped her hooves.

"What do you mean?"

"I'm saying he is an alien! A devil spawn!" Luna hissed, crouching down. Her limbs trembled.

"Devil spawn? He just saved us all, I don't think he's a devil," Rainbow Dash said.

"But he is an alien, so you're right," Twilight admitted. Celestia gasped, locking eyes with her student. Twilight winced, giving a sheepish smile. "Sorry for not telling you, Princess. It was kind of between us."

"And now he's all wacko again. Great," Dash muttered. She flew down and scooped his limp body up.

"What happened?" Celestia asked. "And what was that spell you used, Luna?" She looked at her sister.

"It was just a species distinguishing spell. But he couldn't be identified!" Luna snarled, backing into the wall of the TARDIS. She grunted and looked around the spacecraft. "And now we are all in an alien spaceship!"

"But he looks like a pony."

"Well, he got transformed into a pony when he crashed here. And the reason he's all sick and whatever is because his DNA is changin' because he's not supposed to be here, in a pony's body," Applejack explained.

"Interesting." Celestia narrowed her eyes, looking over at her sister. "And Luna, he just saved us, what are you so afraid of?"

"We are not scared of anything! We are unafraid!" Luna roared, springing up and spreading her wings. Her eyes shone fiercely.

"Then why are you acting like such a scaredy pants?" Pinkie Pie asked. Luna gasped. "You know, when I was scared as a little itty bitty pony, my granny would always tell me to laugh at what I was afraid of!" Pinkie giggled. She brought a hoof up to her face to stifle the next, but ended up laughing loudly. "See?"

"We. Are. Not. AFRAID!" Luna repeated, growling. Then, she sighed. "I have nightmares about what was in space. The aliens, the monsters. They spoke to me! In my dreams! I am the Princess of the Night! I do not get nightmares, or have others in my dreams! I am the one to visit dreams; to stop the bad ones. I still do not understand what happened, but I have defended us from above. But I have failed."

"Oh Luna, why didn't you tell me?" Celestia asked. She went up to her sister and put a hoof around her.

"Because I thought you would laugh." Luna dropped her head sadly.

"It's okay."

"Okay, um, no offense, and sorry, but we have more important issues right now. Like how there's a changeling army and four extremely powerful Queen changeling things or whatever they are and Discord is half dead and the Doctor is changing into a pony and it's going to kill him pretty much so. . . . . yeah," Rainbow Dash said, interrupting. She wiggled the Time Lord in her arms for emphasis.

"You're right. Now, what are we going to do?" Celestia asked.

"I know," Luna spoke up. She raised her head.

"What?" Rarity asked.

"I want to see Discord."

* * *

"Oh my."

Celestia barely managed to get the words out as the alicorns laid their eyes on the broken spirit. He really was a mess; stitches laced through his skin, sealing the giant wound across his stomach. In all fairness, it wasn't an extremely long or wide gash, as Discord had the body of a snake and was exceedingly skinny. Bandages were wrapped around his head and bat wing, plus his upper body.

"This is horrible. ." Luna whispered, eyes watery as she gazed upon the draconequus.

"I agree. I can't believe anypony would ever do anything like this," Celestia murmured.

"Chrysalis is not a pony," Luna hissed. A stroke of her wings later, the Princess of the Night was by Discord's bedside. They were in a small hospital looking room, which really surprised both Princesses as they had went through the hallways, which seemed to stretch forever.

"You are right about that, my sister." Celestia regally walked up to the midnight blue alicorn. The pair gazed down at the unconscious spirit, their eyes sad. The Sun Princess dipped her head, horn glowing dimly. She touched Discord's forehead.

He let out a groan, eyebrows furrowing. (One of them was burned off. It would've been funny if he hadn't been in such a horrible condition). Discord shifted, eyes fluttering open. The first thing he saw was something really colorful and wavy, so what did he do?

Attack it.

He clawed at Celestia, who jerked her head back in surprise. Discord snarled at the alicorn, who tried to get around the flailing arms. She pressed his shoulders back into the small cot, and he relaxed. His blurry vision finally went back to normal chaotic levels, meaning everything was switched around with something else. Like, for instance, Celestia was a giant white dog with a rainbow mane. Sometimes he could control these things; when he was mostly sane, that is.

"I. . . what? Oh, Celestia, it's just you. Why are you here?" Discord asked groggily. "I guess I woke up at just the right moment." He rubbed at his eyes, one of them black and blue.

"Actually, no, I woke you up. The ponies showed us where you were," Celestia told him.

"Ah, the ponies. . I remember." He tried to sit up, but only got about half way. Sighing, he snapped his fingers. A tiny white kitten appeared in his paw.

"What do you need with a kitten?" She watched as it snuggled against the spirit, purring. It licked Discord's thumb.

"I don't know. It's chaos magic. I just know how to read it." He tossed the kitten at Luna. The alicorn caught it, but as the fluffy white ball landed in her hooves, it turned into a shark and made the Princess of the Night get squished under it. She quickly zapped it with a beam of magic before it could take a bite out of her. "By the way, I like the new look. Dog style must be popular. You and Luna are both into it." He smiled in content, closing his eyes, arms crossed. The Princesses exchanged glances.

* * *

After a quick snap of his fingers, Discord was healed. The three had gone back out into the control room. Discord was tackled by a happy yellow pegasus and nearly had his spine broken she squeezed him so hard. But as they settled down, they wanted to know what had happened.

"Well, it's kind of violent. I don't want little Flutter Butter here getting sick and throwing up all over the place," the Lord of Chaos said. He motioned to the mare still wrapped around his waist, her eyes squeezed shut. A happy smile was on her face.

Twilight gave him a frown. "We need to know."

"Alright, alright. But shouldn't we wait until the Doctor wakes up? I mean, he did save me, I'm sure he'd want to know."

"He has a point, ya know," Rainbow Dash mentioned, raising a hoof. She was trying to get the Time Lord's erratic breathing and heartbeats under control.

"But who knows when that will be?" Pinkie Pie inquired. She bounced up to Twilight. "I mean, he won't even wake up for a party! That's ridiculous! Party pooper, that's what I say to that!" She slapped one hoof down on the console, eyebrows furrowed.

"Pinkie, his DNA is trying to change. I'm sure that's pretty painful."

"But we need him to wake up!"

"I doubt he will. I mean, last time he was out for, like, ever!"

"Will you two stop arguing?" Discord snorted.

"What do you suggest we do then, Mr. I've Already Died Once Today?" Dash asked, throwing her hooves in the air.

Discord shot a glare at her, then made a zipper appear over her mouth. It zipped shut. She scowled, then reached up a hoof to unzip it.

"Watch it bub. Don't want to die one more time, do you?" the pegasus growled.

"Maybe I do, how do you know?" Discord retorted.

"I can make that happen!"

"Do it then!"

"Fine! I will!"

"Fine!"

"Fine!"

"Enough!" Celestia shouted, sending a wave of magic pulsing around the room. The ponies cringed and looked over at the Princess.

"Uh, gosh, what was that? My head hurts now, thanks," the Doctor grumbled. He sat up, rubbing his head.

Dash sighed. "Of course."

"What?" He found all eyes on him. He gave a few nervous laughs, then directed his attention to the draconequus. "Um, so, Discord? You're all better, I see. Would you mind telling us what happened?" The Doctor cringed as they all glared at him. "Before looks can kill, please."

Discord cracked his knuckles. "Alright. But be prepared for a horrible story."

_Discord was laying on the ceiling, contently eating a book. _

_"Mm, tasty. No wonder book worms like this stuff," he observed, talking to himself with his mouth full. He swallowed what remained of the cover and burped. He was about to take a nap when the castle began shaking violently. He fell off the ceiling and onto the floor. The doors burst open, and a swarm of _

_changeling drones barged in. They surrounded the draconequus. _

_"Oh, fun!" a voice laughed from the doorway. Discord spun around. Chrysalis stood over Discord, who was still sprawled on the floor. She batted her eyelashes at him, a smirk on her face. _

_"How nice to see you again! But this time you're not in a statue. Tsk tsk," she scolded. "But don't worry, you won't need to be stoned again after what I'm going to do to you!" Before he could react, a large blast of energy shot out of Chrysalis's horn. It hit Discord and sent him reeling back several feet. _

_He groaned. That would definitely be a burden. Until he could heal it, that is. _

_"Chrissi! You came to visit me! I'm," Discord grunted, "so happy!" He managed to put a pained smile on. _

_"I'm glad. Now, breath your last!" She charged up her horn and sent a green laser at the spirit. He jumped out of the way, only most of his antler being sliced off in the process. Discord gasped, touching the stump. _

_"My favorite horn! I look like Elliot! Oh sweet chaos!" He put his hands to his face, feigning offense. "You'll pay for that!" He clenched his paw into a fist, then opened his hand. Hundreds of cards raced at the Queen of the changelings, cutting her and making her grind her teeth together. _

_Discord looked at his paw. "Well, I was hoping for something better than that." He looked up and Chrysalis, letting his paw fall back to his side. "It's been great, but I'll be going now." He snapped his fingers, and he was gone. _

_"Ha! Changelings!" The Queen ordered. She smirked, waiting. _

_About ten minutes later, dozens of changelings ushered Discord into the room again. He had his hands up. _

_"Geez! Never give up, do you?" Discord muttered. He rolled his eyes. He waved his arms around his middle, making a target appear. "Fire when ready!" He waited. The Queen started laughing. _

_"Oh, do you think this is all a game?" Chrysalis asked._

_"Um, isn't everything?" Discord looked confused. _

_"Well, you're a joke. And no, this time it's not!" She flung herself at him before he could move and broke several of his ribs with her massive hooves. She stomped him into the ground. _

_Discord grit his teeth, wincing. He stuck out his tongue and the Queen was suddenly assaulted by hundreds of wasps. She shrieked as they stung her over and over. She swatted at them. Her horn lit up and they were all turned to dust. _

_"You're next!" she hissed. She brought back a hoof and punched him in the eye. Discord yowled, and then made the whole room turn upside down. The Queen cried out in confusion as the room was flipped around. _

_Now Discord was on top of her. He touched her forehead, turning her into a foal. She cried and unleashed a very small bolt of green fire at the draconequus's chest. He was hit backwards, landing on his back with a thud. Discord groaned. _

_She may have been small, but her spells still had the same affect!_

_The Queen changed back into her normal self. When she had blasted him it had reversed it. _

_Chrysalis licked her lips and pounced upon the Lord of Chaos before he could get up. He tried to roll over and get to his feet, but he only managed to get onto his stomach before the changeling took his wings in her hooves. She put one hoof under his bat wing and another on top. Then she brought that hoof down onto the wing, breaking it over the other hoof. _

_Discord yowled in pain, struggling out of her grasp. He wiggled like a snake and shot into the air. He floated there, keeping himself suspended with his magic. He snarled, and the room exploded with fire. Chrysalis screeched in fury._

_"You will die today! Why not just end it now, and not make it worse?" she cooed, looking up sweetly at the draconequus. _

_"Are you sure this isn't a game?" Discord asked. Usually everything he did was a game, or some sort of joke. Mostly to distress others, or cause them emotional misery. But hey, you gotta do what you gotta do. _

_Chrysalis extinguished the flames with her magic, causing the room to go silent. He glared up at the spirit. Her horn flared and the laser shot out, slicing into Discord's body. _

_He yowled, falling to the floor. _

_Blood pumped out of his body. His breath came in shallow gasps, chest rising and falling ever so slightly. He held his side, trying to stop the bleeding. His vision blurred as the world faded more quickly than he could use magic. _

_Chrysalis stalked up to him, looking into his face. "You thought everything was a game. Heh, how wrong you were." Her face was one of contempt as she watched Discord's life seep away_.

"That was very disturbing."

Rainbow Dash was the first one to speak after Discord finished. The room full of ponies sat in shocked silence.

"Yeah, Ah have to agree with Rainbow," Applejack said.

"I think I'm gonna be sick," Twilight muttered, holding her stomach. Pinkie Pie rubbed her back.

"Need a doggy bag?" the party pony asked, getting one out of her fluffy mane. The unicorn looked at her strangely for a moment before slowly taking the bag, all the while keeping eye contact.

"Told you it was violent," Discord chimed. He crossed his arms.

"You really think everything is a game, don't you?" Luna asked.

Discord nodded, smiling. "Of course! Because where's the fun in ordinary life? I much prefer games." He snapped his fingers. A bright flash enveloped the spirit and then he was two. The duplicates smiled at each other and shook tails. Then they fist bumped and exploded into hundreds of bats. They flew up and made a one dimensional Chrysalis, who laughed evilly. The ponies watched, stunned, as the fake changeling's horn glowed, and she vanished.

The room went dark, and then she appeared right behind Rarity.

"Boo!"

"Aaaaahh!" the unicorn shrieked, jumping away from the Queen, who melted into liquid mercury and snaked its way around the room. It then took the shape of Discord, and turned back into him.

Rarity was in Pinkie Pie's hooves, arms around her friend's pink neck. Her eyes were wide. The ponies sat in stunned silence.

"Haha! Oh, Rarity, your face was priceless!" Discord cackled, putting his hands on his knees. He straightened up and wiped a tear from his eye.

"Hehheh!" Pinkie started giggling. "Hehe! You were so scared! And I was scared too!" The party pony laughed, snorting every once in a while.

"So, that matter taken care of, what are we going to do about our sisters?" Applejack asked.

"Yeah! If she hurt Scootaloo in any way, I'll kill that miserable excuse for a bug!" Rainbow Dash snorted, knocking her hooves together.

"Calm down, everyone. We need a plan," the Doctor announced.

"You got one?"

He paused. "No. Never mind. I usually just make it up as I go along. So, I need three ponies to come with me."

Dash raised her hoof. "Count me in, whatever it is. You still owe me for crashing into me with your box."

"I wanna go I wanna go!" Pinkie Pie wailed, dropping Rarity and bouncing up and down.

"Hah! Discord is in!" the Lord of Chaos exclaimed.

"Alright. Follow me," the Doctor said.

"Good luck," Twilight told them as the four headed for the double doors.

"Don't get Discord killed again!" Fluttershy shouted, her face angry.

"We wish you the best of luck. Be brave," Celestia said, dipping her head to them.

"Allons-y!" the Doctor shouted. He opened the doors and the other ones followed.

"So, what are we doing?" Dash asked, hovering above the two earth ponies with Discord.

"We need to separate the changelings. So, Discord, you go down to the kitchen. Rainbow Dash, you wait by the Princesses rooms, and Pinkie Pie, you go down by the main entrance. You got that?" The Doctor turned around as he finished.

Discord saluted mockingly. "Aye aye, captain! Or should I say, Doctor!" He laughed at his own joke.

"Just go." In a flash, he was gone.

"Seeyah. Just hope this plan works," Rainbow Dash said. She flew off.

"Boingy boingy boingy!" Pinkie Pie said as she bounced down the opposite hallway. The Doctor was now alone.

"Alright, here I go," he mumbled to himself. He ran to the throne room, a look of determination on his face. He entered the grand room, pushing the now dirty doors open. The three changelings turned to look at him. They blinked, and then snarled.

"Oi! Your moms all have fleas!" he shouted.

"You-" Sweetie Belle growled. The three mares took a step forward.

"Will be-" Apple Bloom continued. Another step.

"Killed!" Scootaloo screeched. They lunged forward, all their movements the same.

"Ahahaha! Catch me if you can!" the Doctor shot off, heading first towards the Princesses rooms. He skidded around the corners, nearly falling down, but always staying ahead of the changelings. He saw a small blue blob under a table. He looked back and saw the mares. "I'll let you know I do a lot of running!" He took a flying leap over the table and suddenly Rainbow Dash shot out from under it, heading in another direction. Scootaloo glanced at the other two and they nodded. The pegasus took off after the rainbow colored streak, leaving Sweetie Belle and Apple Bloom going after the Doctor.

Soon, the Time Lord was at the kitchen. He ran past a statue, which looked suspiciously like Discord. As the earth pony sprinted past, tie flapping in the wind, the stone broke apart. Apple Bloom went after the silly draconequus, who, as usual, was treating it as a game.

"One more," the Doctor whispered, diving under a fallen pillar. He glanced back and barely moved his head out of the way in time to see a green bolt of lightning coming towards him. It struck the stone beside him and the Time Lord gulped. Sweetie Belle was lighting up her horn again.  
The Doctor saw he was nearing the main gates. A flying pink shape bounced out, distracting the changeling. Pinkie Pie pulled out her party cannon and blasted Sweetie Belle. The mare ignored her and continued after the Doctor but found he was gone.

* * *

The Doctor smirked, holding his sonic screwdriver in his hoof. He kissed it and stuck it back under his collar, then went through the large golden doors. Queen Chrysalis's head shot up, and she frowned.

"I thought I'd gotten rid of you!" she growled. Her slitted eyes narrowed.

"You thought so," he said, grinning, "but, I have something. Something that maybe is bad for you?" He took out the spray bottle, tossing it into the air.

"That?" she scoffed.

"Yes, this." He held it up for her to see.

"And what exactly is that?" She looked at him, bored.

"Oh, nothing really. ." He pressed his sonic screwdriver up to it and clicked a button, holding down the trigger for the spray bottle. A large flame came out, and suddenly Discord, Rainbow Dash, Pinkie Pie, and the three changelings were in front of them. They all looked pretty shocked at being there.

"You three, duck!" he shouted.

The changelings knew what was happening too late.

They were blasted, the fire burning at their flesh. They thrashed in agony, trying to escape the burning. The smell of cooked meat filled the room, and smoke drifted up through the broken windows and roof. As soon as the screaming died down, the Doctor stopped. He waited for the smoke to clear and grinned.

Three young fillies lay dazed, on the floor. The Doctor laughed, running up to them. He quickly picked them up. The other three stood up, confused.

"You did it!" Rainbow Dash exclaimed, swooping through the air and picking up Scootaloo with glee as soon as she saw the filly. She snuggled the orange pegasus happily.

"I'm not even sure what that was, but great!" Discord cheered. He threw his paws up in the air.

"Ooh, fun!" Pinkie Pie giggled.

The Doctor smiled. "Come on, let's get back to the TARDIS."

"Wait, where's Chrysalis?" Rainbow asked, seeing the Queen was gone. She held Scootaloo a little closer to her.

"You'll see."

* * *

_**. . . *wink wink* **_


	7. Well, think again

"So, um, where is Chrysalis?" Rainbow Dash asked uncertainly, hovering above the Doctor. She still held Scootaloo tightly to her chest. The filly was still dazed, her eyes half closed.

"Just wait. I don't want you to panic," the Doctor told her. He swerved around huge chunks of marble pillars that had been crushed. Dash herself ducked under the ones leaning haphazardly against the walls and ceiling.

"We might panic?" Discord asked, eyebrows raised. Then, he frowned, a deadpan look on his face. "She's in your TARDIS, isn't she?" The three stopped at the blue wooden doors. The Doctor placed a hoof on one. Screams sounded from inside the spacecraft.

"Yep." He pushed the door open and stepped inside, with Discord and Rainbow Dash trailing closely.

The ponies were backed against the wall, the ones with horns having theirs lit brightly, ready to fire. A loud hiss sounded from the other side of the ship, and the three who just entered looked over.

Chrysalis was hovering in the air, bright green magic covering her horn. She had a fierce glare on her face, eyes burning. She saw the Doctor and growled.

"You! What have you done?! Where am I?!" the Queen demanded angrily, her magic glowing brighter before it unleashed its fury. Discord quickly teleported them out of the way, to the rest of the group.

"Hello Chryssi! Nice to see you again!" the draconequus chimed. He snapped his tail fur, and then the changeling was knocked out on the floor. He turned to the ponies, smiling. "Oh, girls, forgot to tell you, I was expecting!" Two small bundles swaddled in blankets were held in the crooks of his arms.

"Sweetie Belle!" Rarity exclaimed, taking the filly out of Discord's grasp. The blankets vanished and she hugged her little sister tightly. Her large sapphire blue eyes were squeezed shut, tears leaking out of them, smearing her makeup. A tight frown was on her face.

"Apple Bloom! Oh, thank goodness she's alright," Applejack sighed, reaching up for her sister also. Discord handed the filly to her.

"Why was Chrysalis here?!" Celestia demanded, glaring at the Doctor. She loomed over the smaller stallion, who lowered his ears, a timid look on his face.

"Um, well, it was how it all worked out. . ." the Time Lord squeaked. He waited until the angry Princess backed off, and scurried to the sleeping changeling.

"Alright, I think we'll be good for a while. She seems like she's sleeping pretty deeply." The Doctor walked back over to the ponies. "Are the fillies waking up yet?"

Applejack shook her head. "No. They seem to be in a kind of, what do you call it. . . stasis mode." She motioned to how Apple Bloom was laying limply in her arms, eyes half closed.

The Doctor bit his lip. Not wanting them to see how worried he was, he turned around again.

"So, uh, what now?" Rainbow Dash asked, shrugging.

"Well, I say we wait until Chrysalis wakes up, and we get some answers."

* * *

The Queen shifted, her head aching dully. She sat up, stretching her legs. She opened her eyes, and was immediately faced with a load of angry mares. She blinked once, then smirked.

"And it's not even my birthday!" she cooed.

"Silence, Chrysalis!" Luna shouted loudly. The Queen gave her a glare, but held her tongue.

"What have you done to the fillies?!" Rarity demanded, wanting to know why her little sister was not waking up.

"Like I'd ever tell you!" she snapped.

"Chrysalis, you will tell us what you've done," Celestia said firmly.

The Queen smirked. "What makes you think that?"

The Doctor glanced up from the TARDIS console. "This." He pulled a switch, and high pitched sounds radiated through the ship. Chrysalis hissed, holding her head.

"You'll never get me to talk!"

"Suit yourself." He turned a dial, raising the pitch even more. The changeling winced.

"Uh! What do you want to know?" She stood up and faced the ponies.

"What's wrong with the fillies?!" Rainbow Dash demanded, shaking her fist at the Queen.

"It's simple, really. Just the aftermath of the spell. I can turn them back to normal, if you want," Chrysalis said innocently, blinking. The ponies exchanged suspicious glances.

"Change them back," Celestia ordered. Chrysalis smirked evilly, then lit her horn. The Doctor's mind raced, the possibilities of what he thought would happen actually happening.

Meanwhile, green magic was seeping into the fillies. They twitched slightly, and their eyes opened. They were still like the Queen's. The three fillies leaped out of their sisters' arms and stood in a line.

"What are you doin'?!" Applejack shouted. She reached out for Apple Bloom but a field of energy stopped her.

"I'm changing them back, of course!" Chrysalis cackled. She fired three small shots at the fillies, and then they began to grow. Their limbs stretched, holes forming in them. Sweetie Belle's horn grew twisted and Scootaloo's wings lost their feathers and turned transparent. The fillies' manes grew longer and holey. Shiny carapaces formed slowly over their backs. Their teeth sharpened and poked out from their top lips.

"Quick! Get behind me!" the Doctor yelled, bouncing forward. He took out his spray bottle and sonic screwdriver, preparing to fire the fillies back to stasis mode. The Queen laughed, and the two objects were yanked out of the Time Lord's hooves.

"What interesting items! How do you use this?" Chrysalis inquired, smirking. She inspected the sonic screwdriver. She tried random codes until she grew bored. She held up the spray bottle, pointing it at the group of ponies. "Let's see what it does to you!" The sonic lit up and the fire shot out of the end of the bottle. The ponies ducked, barely escaping the blast. The Doctor grunted in pain as he hit the floor, but managed to stay awake. He crawled up and ran at Chrysalis, attempting to knock her away. She saw him and teleported to the side. The stream of fire enveloped the Doctor, who shouted in pain. His skin burned, the smell of cooking flesh filling the air.

"Doctor!" Rainbow Dash exclaimed, flying forward. She tried to go through the fire, but found the sweltering heat too much for even her. She squinted her watering eyes, trying to see the Doctor through the blaze.

"I'll get him out!" Discord proclaimed, snapping his fingers. The Time Lord appeared off to the side, his mane on fire. A bucket of water appeared above him, and drenched the earth pony. The Doctor fell to the floor and lay limply.

"Now! Let's go, my pretties!" the Queen cackled to the other changelings. "And bring the Doctor!" Scootaloo flashed forward and picked the Doctor up by his scruff. He curled in a ball, trying to stop the searing pain as the changeling flitted towards the others. Chrysalis saw the Princesses' horns glowing, and held up a hoof. "If any of you foals try to get the Doctor back, I'll have my three children here kill him!"

As if to prove her point, Sweetie Belle flared her horn and Apple Bloom snarled menacingly.

"We're off!" She kicked open the blue doors and the four changelings disappeared into the dark castle.

The group of ponies stood, or in Rainbow Dash's, Fluttershy's, and Discord's case- hovered- in stunned silence.

Pinkie Pie was the first to speak. "What just happened?"

* * *

"What are we gonna do? We have to rescue him!" Rainbow Dash exclaimed, throwing her hooves in the air.

Applejack stepped forward. "She's right y'all. We need to make a plan." The ponies exchanged glances.

"How? Chrysalis said she would kill him if we tried to get him back," Pinkie Pie pointed out. Twilight Sparkle looked over at the party pony.

"Pinkie's right; but so is Applejack. We can't just leave the Doctor with the Queen. But how would we even get him back anyways?" Twilight asked.

"I could just snap my fingers and we'd have him back," Discord mentioned, pressing his fingers together.

"But then the Queen could get him right back," Celestia said. The ponies looked over at her. "And if she did, she'd kill him."

"Great, just great," Rarity mumbled. "We're now stuck in this box, with Chrysalis doing who-knows-what to the Doctor, and the fillies are once again changelings."

"Well, we're not technically _stuck _in here. We could go and beat the fudge out of Chrysalis and get the Doctor back before the fillies, well, not anymore, kill him. Then we could find out how to change them back to normal," Rainbow Dash suggested. A few deadpan glares were directed her way. Dash shrugged. "What? It could work."

"I really don't think so. Chrysalis has gotten stronger than when we last met, and we've all seen it," Luna reminded.

"Then what are we to do?" Rarity inquired.

"I'm afraid the Doctor is on his own," Celestia informed.

* * *

"Put him in the cage, and make sure he does not escape," Chrysalis ordered, walking regally past the three other changelings. They blinked and Scootaloo flitted forward to the large metal cage. She deposited the Doctor inside, closing the door. Sweetie Belle clicked the lock closed. The three stationed themselves in front of the cage, blank glares on their faces.

The Doctor was still, not daring to move a muscle, even if it was nearly impossible right then. He felt his pelt crawling; a side effect of the fire, no doubt. But it wasn't just fire, he knew very well. It was a special formula he himself had designed using information from Twilight Sparkle about the dragon, Spike.

Its duties were to transform and/or transport, and that was exactly what was going on. But instead of changing him into a pony, it was trying to change him back into his original Time Lord self. That was good, but at the same time bad, as he did not know if that was allowed. Plus, he didn't need a bunch of ponies seeing what he truly looked like.

The Doctor managed to keep in his whine of pain as fingers began growing out of his hoof. The transformation was not quick and short like in the TARDIS; it was slow and painful now, without her help. He winced when his leg bones began changing shape. They started to straighten out, taking the shape of a human's. He wanted to growl in frustration but kept his mouth firmly shut. He didn't want to risk the changelings turning around. The crack of the bones nearly made the Doctor think they would turn around, or Chrysalis would come back from where ever she went.

His ears began shrinking and changing shape, becoming more round and less pointed. They went to the sides of his head as his muzzle came in. He clenched his teeth, grimacing.

* * *

"We can't just leave him!" Rainbow Dash barked angrily, fluffing her wings out boldly.

"There's nothing we can do, Dash," Twilight firmly told the pegasus. Rainbow growled, flicking her tail.

"Oh yeah? Well, I'll show you guys! I'll go save him!" She sped towards the doors and hit them open, leaving the TARDIS. Pinkie Pie bounced forward, but Rarity held onto her tail with her magic.

"I can't let you go after her, dear," the unicorn said sadly. The pink pony stood up on her hind legs.

"But we can't let her go alone!" Pinkie protested, pawing at the air with her front hooves.

"Rarity's right, Pinkie," Applejack told her. "It's too dangerous."

"I can take whatever's out there!" She bounced wildly, teeth clenched.

"I couldn't stop her in time, but I managed to put a harm-free spell on Rainbow Dash. She will be safe for the time being," Luna announced. Celestia locked eyes with her and dipped her head without saying anything.

"Thanks, Princess Luna," Twilight said, bowing. She turned her head to the still open doors, and closed them.

"Now we wait, I presume," Rarity sighed.

* * *

Rainbow Dash rocketed through the broken castle, dodging fallen pillars and collapsed walls. Her spectrum mane whisked out behind, creating the signature trail that nearly always followed the pegasus. Her face was set in one of determination; eyebrows furrowed and a tight frown on her lips.

Dash didn't know why she was risking her life to save the Doctor. She really didn't. Maybe it was her sense of loyalty, or her desire to be a hero.

But as she flew circles around the hallways and corridors, her heart thumped in a way she had never experienced. She'd never felt like this before, and Rainbow didn't know what she was feeling.

Feather flu?

No, she'd had that before.

* * *

The Doctor was in silent misery. He was partially back to normal; only his tail and spine not changing. He had clothes on, for some reason. He presumed that as some sort of side effect, his tie contained his ability to wear them. Thank goodness it had not been burned all the way off in the fire.

The three changeling fillies stayed in front of the cage, not turning around, thankfully, once during the transformation. They stood still as stone, blinking and even breathing together. They were all linked by some sort of magical trance, the only differences being the obvious.

"Hey! Feather-brains!" a loud, brash voice called. Lavender, green, and sunset pink-and-orange cat-like eyes flashed over to the rowdy blue, rainbow-maned pegasus hovering in the cracked doorway. Identical hisses were directed at Rainbow Dash, before Sweetie Belle's horn crackled with its shimmering green aura. A large bolt of lightning shot out at the pegasus, who easily dodged it and ended up next to the broken stained glass windows in the blink of an eye. She waved nonchalantly and smirked at the changelings.

They all hissed again.

"Too slow! Come on, you don't stand a chance if that's how you're gonna fight!" Rainbow Dash mocked, hooves by her mouth to direct the sound. She then put her hooves by her ears and wiggled them, sticking out her tongue. A flick of her wings later and she was on the other side of the room. Another flash of light later and a smoking hole was burnt right above Dash's head. She laughed, shaking her flank at the changelings.

"Missed me, missed me, now ya gotta kiss me!" Rainbow called. Scootaloo launched forward now, narrowly missing her idol. The pegasus darted backwards, and prepared herself for the changeling's next attack. She held her hooves outwards, as if she was going to catch her. Scootaloo snarled and dived towards the blue pegasus. Rainbow side-flew and stuck her hoof out just as Scootaloo missed her. Her hoof went through a hole in the filly's pinkish insect wings, the timing so perfect that Dash's hoof didn't even touch the sides of the hole.

Scootaloo opened her mouth in surprise. She went around her own wing, falling from the air. Rainbow Dash yanked her hoof back, leapt forward, and started forming a tornado. The speed of the winds soon caught the changelings in its force, and they tried to grab onto something as they were tugged back into the swirling vortex. The colors blurred together.

Rainbow Dash rocketed out of the tornado and screeched to a halt in front of the grey, metal cage. She bucked the cage door open and stopped in surprise. Her mouth popped open, eyes wide. She blinked a few times in quick succession, trying to make sense of what she was seeing.

The Doctor cringed as he saw the look on Rainbow Dash's face; she was horrified. He tried to scoot back in the cage, but found he was already against the wall. He averted his gaze and waited.

"Wha-what? What happened? Is this. . . your true form, or what?" Rainbow Dash asked, leaning forward to poke the Time Lord.

"Uh. . almost. My spine is all messed up, and I still have a tail," the Doctor answered slowly, wiggling his tail at the end for emphasis.

". . Whatever. We have to get going! Come on!" She turned around, but realized he wasn't following. "Can you walk?" She watched as he struggled to stand on his feet. He had crawled out of the cage, and was now leaning on it as he tried to take a step.

"Uh. . ." The Doctor fell onto his hands and bent his knees so his feet were still holding him up. He took a few steps and sighed. "I'll have to crawl. Now, lead the way!"

"Alright. Just shout if you need help. I'll keep an eye on you though." Rainbow Dash took off, glancing back over her shoulder every once in a while to make sure the Doctor was keeping up. His long brown coat flapped behind him, concealing his tail as he crawled. His head was down, and his messy brown hair bounced up and down like Pinkie Pie's did.

After a few minutes, Dash looked back again. She hear snarling and gasped, seeing the changelings at the end of the corridor.

"Quick! We need to go faster!" the pegasus ordered, waving her hoof to take a side path. The Doctor grunted, following after her. He glanced up, panting.

"Gosh! How did I do this for that long?!" he growled. "Crawling is exhausting!"

Dash noticed the quickly approaching fillies and sighed. She dropped back and scooped up the Time Lord in her arms, picking up the pace. He clung to her neck as she dipped and swerved, trying to lose the changelings in the hallways and debris.

It was when she tossed him into the air, over a pillar, catching him on the other side, that he officially felt sick. He closed his eyes, feeling the pegasus do a loop-de-loop around some stairs.

"Oh, are we almost there?" he groaned.

"Actually, yes!" Rainbow Dash replied, her words being sucked back in the air at the pace she was flying. "Hang on!" He felt a large crash, and himself almost falling, and opened his eyes.

The Doctor smiled; seeing the inside of the TARDIS was comforting. Dash set him down on the small red chair by the railing. He could feel the eyes of every single creature in the room on him, but he didn't care at the moment. The Doctor managed to get off the chair and limp, practically falling, onto the controls. He smiled with relief, and ran his hands (oh, how good it felt to have hands again)! over the numerous buttons, knobs, and switches on the console. He did this for a few good minutes before he had to sit down because of the pain in his back.

He leaned back leisurely, putting his arms on the top of the chair. "Yeah, this is what I look like; minus the tail, and weird back. Not totally finished with the process yet," the Doctor said.

"So. . you're definitely an alien, huh? No denying it now," Twilight Sparkle half-joked, rubbing her hoof along the ground. She glanced away nervously.

"Awesome! Now I can throw a 'I found out what aliens look like' party!" Pinkie Pie cheered, hopping up and down in the air excitedly.

The Doctor gave her a frown. "No, I really don't think so." He winced, feeling his spine realigning. "I'm not going to eat anybody, if that's what you're all afraid of now," he commented after a couple more minutes of awkward silence. His tail started disappearing.

"So. . ." Rarity started, "are you still at danger from turning into a pony now?"

"I shouldn't be. At least changing back lets me escape that fate." He let out a gasp, arching his back after a wave of pain ran up his spine. He gave out a long, shuddering breath when the pain finally passed.

"You alright?" Rainbow Dash asked, concerned.

"Yeah; it's just my spine repositioning itself."

"Just?" Applejack coughed.

". . Yeah." He looked at the southern pony. "So, what now? Queen Chrysalis stole my sonic screwdriver."

"Hey! I just got an idea!" Twilight announced. "If we find out the counter spell, the one the Queen has on the fillies, then we can change them back to normal! Then, we can defeat her and her changeling army."

"Alright! Out of the TARDIS-"

"Got it," Discord called, holding a book in his paws.

The Doctor sighed. "Sometimes you just take the fun right out of an adventure."

* * *

_**Gosh, my chapters are really starting to lack detail. . . *sigh* **_

_**Ohohoh, amazing none-the-less! I love parts with the Doctor getting kidnapped! **_

_**And by the way, Rainbow Dash's feelings are EXACTLY what you think they are! This is a ROMANCE after all. **_


	8. Okay I'm pretty sure this time

**_Oh boy, you guys are going to love this chapter! _**

* * *

The Doctor took the thick, brown leather book from Discord's mismatched paws. He grunted as he almost dropped it; the thing was heavier than it looked! Flipping through the yellowed and torn pages, eyes scanning every word in less than a second, the Time Lord searched for the spell. He stopped and grinned.

"Okay, here it is. Who here can do it?" the Doctor asked, looking at the ponies who were clustered around him. Twilight Sparkle stood on the tips of her hooves, trying to get a better look at the spell. Applejack, whose shoulder the unicorn was looking over, stepped out of the way, irritated by her friend invading her personal space. Twilight toppled over from the sudden movement, but quickly got back on her hooves. She let her eyes scan it for a few more moments.

"I don't think I can do that one that powerful," Twilight said, shaking her head. She turned her head to her mentor. "You can surely do it, Princess."

Celestia closed her eyes sadly. She shook her head as well. "That is a dark spell. It's black magic. I can only do simple things of black magic, as Sombra did. Nopony can do that."

Discord grinned. "Well, it's a good thing you've got me then!" He floated on his back and leaned backwards over the ponies, cracking his knuckles.

"Discord, are you sure? Your magic is very strong and uncontrollable, it would not end well if it did not perform its duty." Celestia watched the spirit warily.

"Oh, please! I may not have control every once in a while-"

"Don't you mean half the time?" Applejack snorted into her hoof. Discord shot her a glare. The earth pony was transformed into a box of cereal. (wink wink)

"Discord!" Celestia shouted.

"Whoops," Discord smirked, snapping his fingers. Applejack growled and went to stand beside Rarity. "Anyways, where was I?" He paused. "Oh yeah! That spell! I can do it; no problem."

"Are you completely sure? I don't want anypony getting hurt." The Princess gave him a concerned look.

"I am completely sure! Now, show me the spell again, Doctor." Discord leaned in closer, preparing to snap his fingers. The Doctor lifted the heavy leather book up to the draconequus's face. Discord snapped his fingers, and there was a bright flash. When it was gone, every pony in the room glanced around, rubbing at their eyes, when a pained yelp caught their attention.

Discord was now fighting a shadow figure of himself- and losing. The shadow Discord grinned evilly and punched the real Discord in the mouth, knocking his fang out. The real one rubbed at his jaw and cast a spell, causing the other to start on fire. It squealed and put the flames out, then pounced onto the real draconequus. It held him down and conjured up a huge fist to smash Discord in the face. . . repeatedly. A bolt of lightning struck the shadow, causing it to lose its grip. Discord threw it off and leaped at it, the claws on his lion paw unsheathing. He crashed into the shadow's stomach and dug his claws into its flesh. It fell backward, and managed to fling Discord off. The copy then summoned a huge rock and chucked it at the spirit, catching him in the chest. There were a few cracks heard, and Discord stood up dizzily. He shook his head like a dog and blinked.

"Aw man! I just broke those!" Discord exclaimed. His chest exploded outwards. The broken ribs turned into snakes and flung themselves at the shadow, biting and constricting it. Discord watched in satisfaction, his skin knitting back together, no blood or anything. The copy choked, and in a snap of its fingers, the snakes were harmless worms. They fell to the floor.

"You'll regret that!" the shadow growled, sending a huge wave of water at the actual Discord, who yowled in surprise as he was caught in the wave. Once the water was gone, the copy went up to the drenched spirit, who was laying on the floor. It opened its mouth, and started sucking everything into it. Discord cried out in surprise and tried to hang onto the railing to escape the gaping maw that was his copy's mouth. The suction was too strong though, and the real draconequus was sucked into the fake's body. The copy grinned, eyes flashing brightly.

"I think you'll find that _you _will be the one regretting that," Pinkie Pie said happily, bouncing. The shadow spirit snorted, shrugging.

"And why would that be?" it asked, raising an eyebrow. A flash of yellow and pink bowled the shadow over, a high pitched shriek of fury piercing the eardrums of every life form in the TARDIS.

When the dust cleared from the landing, Fluttershy was sitting on top of the shadow Discord, delivering sonic-speed blows at its face.

"You. Do. Not. Touch. DISCORD!" Fluttershy screamed, picking up the copy by its tail and banging it on either side of her. She spun in a circle and let it fly, hurling it at the ponies by accident. The group quickly got away; Rainbow Dash picking up the Time Lord before he could get away himself.

Fluttershy let out an earsplitting roar which beat the volume she had at the Grand Galloping Gala. She burst forward and pounded the still shocked spirit into the floor farther. She leapt into the air, putting her hooves together, and came down onto Discord's evil twin. It shrieked in pain and the real Discord came flying out of its mouth. He landed squarely on his back and slid, as he was still wet from the wave and from being inside the other him.

Fluttershy gave one last kick into the fake Discord's side, spitting on it as she did so. "Nopony messes with my spirit." She watched as the copy dissipated into particles, blowing away like dust in the wind. The usually timid pegasus turned her back, a stern look on her face. She stormed up to Discord, who was still groaning, curled up in a ball. Fluttershy bent down, her face suddenly full of compassion.

"Oh sweetie, are you okay? You're not hurt too badly are you?" she asked, helping him sit up.

"I would be. . . but you beating the fudge out of the other me didn't help when I was inside him," Discord groaned. He coughed a few times and stood up, using his wings to help keep him right side up. His eyes went in opposite directions for a few moments before he lost his dizziness. "I am. . . I am alright. It's all good, everypony." He bent over and put his hands on his knees, his breathing wheezy. He brought his head up again. "It's all. . . good. ." He slumped over, unconscious. Celestia quickly lit her horn, catching the spirit before he hit the floor. She lifted him over to her, laying him sideways over her back.

"I called it! I totally called it!" Pinkie Pie exclaimed, hopping wildly. All eyes went to her. She put a hoof up, closing her eyes. "Okay, we all called it, but I still did."

"His magic is completely unfit for a direct spell. He usually just does whatever, no spells, just chaos. I shouldn't have let him even try. ." Celestia murmured.

"It's okay Princess. We'll figure out some way to fix this," Twilight comforted.

"I'm sorry to say this, my most faithful student, but probably not. None of us can do a black magic spell like that, I'm afraid."

". . I can," a small voice spoke up. Every pair of eyes went to the Princess of the Night. Luna winced, crouching beneath the burning gazes of the ponies.

Celestia walked forward, and the crowd parted, letting her approach her sister. She loomed over the smaller alicorn. "Luna. . How is it you know how to do this?"

"I. . I am the entity of the Night. I was born with the power of black magic. I was told to keep my powers secret from everypony, and that included you," Luna started, standing up taller. "I am very skilled at black magic, and can do nearly every spell, including this one. If I must use my powers to save Equestria, then I shall." Her eyes sparked for the first time in a while. Celestia gave her a smile.

"Then get to work, sister! We must defend our kingdom!"

Luna nodded and the Doctor immediately showed her the book from where he was still in Rainbow Dash's arms. She narrowed her eyes, reading it over and over in her mind. She leaned her head back, eyes shut this time. Her horn lit, the magic darker and making a whirring sound. Black flashes of lightning broke away from her horn, and the ponies backed away. Luna rose into the air, a few droplets of perspiration on her forehead. She held out her arms, wings flapping instinctively. She opened her eyes, and they were completely black. The room flashed once.

* * *

"You didn't kill them, did you?" Chrysalis asked, putting her hooves together. She leaned back in her throne. The black and dark aqua marble beneath her shone. She looked down at the drone in front of her.

"No, we didn't. They are at your disposal," the drone responded, dipping its head. Chrysalis smiled, sharp fangs gleaming.

"Good. Cadence and Shining Armor will regret ever being born by the time I'm done with them!" she cackled. She turned her head to the three changelings by her side. "I still cannot believe you let the Doctor escape. Disgraceful." She hissed at them. All three heads turned to look at the Queen at the same time. Their eyes flashed once, and then their bodies started glowing.

"What! What is this!?" The Queen put a hoof up to her eyes to stop the blinding light. The changelings rose into the air, and started shrinking. "No! Do not change back!" She leapt off her throne, lighting her horn. A blast of magic crashed into Chrysalis, hitting her back. The fillies fell onto the floor, back to their normal selves. They opened their eyes, blinking. Chrysalis stumbled to her hooves, preparing her spell. Another flash, dark blue this time, took the fillies. They were gone.

* * *

Luna lowered back to the floor, her horn smoking. Her eyes were back to their normal aqua color, shining in the dark TARDIS. Before anypony could react, Rainbow Dash, Rarity, and Applejack had something in their hooves.

"What happened?" Scootaloo asked, confused. She looked around, stopping as she saw what she was sitting on top of. Two brown eyes blinked at her. She froze.

"Nice to see you, too," the Doctor said, rolling his eyes. Scootaloo sat motionless on his chest. "Can you put me down?" He glanced up at Dash.

"Can you walk yet?" the cyan pegasus asked.

"I should be able to now." Rainbow set the Doctor down, taking Scootaloo from his hands.

"Oh Scootaloo! I'm so glad you're back to normal!" Dash exclaimed, hugging the filly tightly. Scootalo blinked in surprise.

"Um, okay? What did we do this time?"

* * *

"Okay, now that that's taking care of, what happens next? Chrysalis is still out there," Rarity said, holding Sweetie Belle in her lap. The ponies exchanged glances.

The Doctor paced the TARDIS, hands in his pockets. "Well, I say we stop her."

Rainbow Dash sighed, face-hoofing. "Any other suggestions?"

"Of course!" the Time Lord exclaimed as if it were obvious. "But I need to give her a chance first."

"A chance?! You're kidding right?! She's evil! We just have to go in and stop her!" Rainbow Dash slammed her hooves together.

"Sorry to be so crude, but I agree with Dash. We can't just let her go!" Rarity agreed.

"Yeah! Let's beat the flank off Chrysalis!" Scootaloo shouted, buzzing her wings. Rainbow high-hooved the filly.

"I always give them a chance," the Doctor said firmly. He took off his coat, throwing it over one of the support beams in the TARDIS. He went up to the controls and pressed a few buttons, and then walked back to the doors. He glanced over his shoulder. "I'll be back. Don't leave the TARDIS. As long as you're in here, you'll be safe." The Time Lord opened the door.

"Oh no you don't!" Rainbow Dash growled, flying forward. She hit the Doctor out before he could react.

"Rainbow Dash!" Rarity shouted, following. The others traded glances, then shrugged. All the ponies raced out the blue doors, and they closed behind them.

The Doctor quickly fumbled in his coat pocket for his sonic screwdriver. The TARDIS began dematerializing. The Time Lord stopped, eyes widening.

"Chrysalis still has my sonic screwdriver!" he exclaimed in distress. He leapt forward, taking the TARDIS key out of his pocket. But he was too late. The spacecraft disappeared. The Doctor stumbled, falling to one knee. He sat there, breathing heavily for a few minutes.

"Doctor?" Fluttershy asked. She slowly approached him, and lay a hoof on his shoulder. He spun around, standing up. The yellow pegasus squeaked, backing off.

"You couldn't've just stayed in the TARDIS, could you!?" he shouted, throwing his hands in the air. He then pointed his finger at Dash, storming up to her. "I said 'stay in the TARDIS, you'll be safe there!" but noooo," he complained, drawing the word out, "you just had to follow me out! Do you not think!?"

Rainbow Dash gasped. "I wasn't going to leave you! What if you got hurt?"

"I can handle it on my own! I've been alone for hundreds of years; you think I can't get out of a jam without someone to help me?"

"I never said that! But what's bad about having somepony help you? It'd make it a heck of a lot easier."

"Girls, girls, you're both pretty! What I'm wondering is why the TARDIS just left us!" Pinkie Pie chimed. She pointed a hoof at where the blue box had just dematerialized from.

"It was the Emergency Protocols. If I didn't make it out, then the TARDIS would take you somewhere safe," the Doctor answered.

"That's mighty kind 'a ya," Applejack started, standing on her hind legs and looping an arm around the Time Lord's shoulders, "but we are the Elements of Harmony. We've been through hell and gone-"

Pinkie bounced in front of her, "defeated evil forces-"

Rarity flipped her mane, "helped the less fortunate-"

Fluttershy leapt into the air, "given love to those who need it-"

Rainbow Dash did a kick flip, "shown some mercy and none-"

Twilight lit her horn, "and stuck together through it all-"

They all finished in perfect harmony. "And we're ready for anything!" At the end, the Mane Six were standing together, determination showing on all of their faces. The Doctor stood there, silent.

"Nice little speech ladies, but it was a might boring for my taste," Discord yawned, putting a paw to his mouth. He sat up straighter on Celestia's back, popping his own.

The Sun Princess smirked. "I hope you had a nice nap," she said, raising an eyebrow.

"Oh, the bed was a bit lumpy~" He gave her a snarky smile, only to be picked up and thrown across the dark castle room. He grumbled something under his breath, standing back up. He brushed some dust off his shoulders and hovered in the air.

"So, Doctor, do you trust us to help you?" Twilight asked, sticking her hoof out to him. He looked at it for a moment, before smiling. He grabbed the purple appendage and shook it.

"Then what are we waiting for?" the Time Lord smirked. "Allons-y!"

"Oh boy! Allenzy!" Sweetie Belle exclaimed, bouncing in the air. She stopped. "Wait, what does that mean?"

* * *

Chrysalis was absolutely outraged. She was fuming. Smoke literally blowing out her ears, eyes glowing with fire, she took out her anger on the nearby throne. She destroyed it in a huge blast of lime green magic, the marble chunks flying in all directions. She snarled loudly as a few bits smacked her from the impact, but stayed still, making no attempt to get out of the way. Her horn still smoking, she flew up to the window, glaring at the destruction. She was about to go and kill she was so angry, when she heard approaching steps. She spun around, hissing. The Queen stopped abruptly when she saw a strange creature leaning against the door frame, arms crossed. It watched her, eyebrows raised.

"What are you?" she growled.

The thing gave her a blank stare, then couldn't contain its laughter as it smirked. After a few moments, it looked back up at Chrysalis.

"Don't remember me, huh? Well, I don't blame you, I guess. I am different, thanks to you," it said as if it were obvious.

Chrysalis narrowed her eyes, then gasped. She took a step back, horn beginning to glow. "The Doctor? You're the Doctor?"

The Doctor smirked. "Yup." He pushed off the door frame and put his hands in his pockets, taking a few steps around. He saw the half melted throne and walked over to it. The Queen glared, but stayed away, not wanting to see what he could do if he got mad. She didn't know if he had weapons or anything with him.

"That formula I cooked up really changes things, huh? Didn't do much work on your spell, of course, but I wasn't under a spell. It was just the laws of the land. Everything has to be a pony; or pony-like, in your case. Well, okay, that's not true, Discord isnt. . ." The Time Lord paused, rubbing at his face with a hand. He closed his eyes momentarily, putting his hands up. "Okay, ignore that. Just- uh, whatever. Equestria is so odd." He turned his back and ran a finger down the smooth surface of the melted marble. He studied it for a while, then turned around. He started approaching the changeling, who snarled. Her horn shone brighter.

"Look, Queen Chrysalis, I don't want to hurt you. But if you don't stop this now, I can't guarantee that you won't be," the Doctor said. He looked her in the eyes.

"And I cannot guarantee that you won't be!" Chrysalis cackled, picking the Time Lord up with her magic. He whistled, and before the changeling knew what was happening, all ten ponies, plus Discord riding in on a wave that followed him only, barged in. She narrowed her eyes, snorting. She backed up to the corner of the room with her prisoner. She made a knife appear, and held it up to the Doctor's neck.

"Stay back, all of you!" she snapped. She pressed harder on the Doctor's neck. "And Discord, get that stupid wave out of here, or I'll kill you again!" The spirit grumbled something to himself before falling back to the floor, the water gone.

"Now," Chrysalis started sweetly, "if you want your precious _Doctor _to live another day, I advise you all do as I say." She smiled evilly. Then she looked up at the Doctor, who was still suspended in her magic grip with the blade at his throat. "I think I'm getting tired of holding you." She brought him over to a high hook and hung him by the back of his suit. Then she made rope appear on his limbs, leaving the Time Lord unable to move.

"Oi! Is this really necessary? Can't you just put me in a cage or prison cell or something? I don't want my suit to rip," the Doctor told the changeling. He wiggled slightly in his bonds.

"No, it is more amusing like this." She gave a few evil laughs.

"How about I make a deal with you?"

"What kind of deal?" She narrowed her slitted eyes at the Time Lord.

"Well, you know that thing you stole from me earlier? Silver with blue on it?"

"That? What about it?"

"Well. . ." he started, "I'll trade myself for that. Just give it to the ponies and you can keep me. And I'll do whatever you want."

"What?! Doctor, what are you doing?!" Rainbow Dash exclaimed, flying higher into the air.

"You can't just give yourself away for that little pen thing!" Luna argued.

"We need you! Don't be a silly pants!" Pinkie Pie shouted. She then laughed. "It makes more sense, because you do wear pants!"

Rolling her eyes, Twilight looked up at the Doctor. "Don't be ridiculous. We'll get you back some way!"

"No, I have to do this. The sonic screwdriver is the only thing that can get into the TARDIS," the Doctor said.

"Enough!" Chrysalis silenced. "Is that all?" She turned to the Doctor.

"Yes. But I want you to leave everyone in here alone as well. That's it." He nodded firmly, finishing his sentence.

The Queen pondered it for a few minutes, then closed her eyes. "Fine. Take it." Chrysalis took the wanted item from her mane. She tossed the sonic at Fluttershy, who squeaked and pushed herself into the floor as the screwdriver landed in her mane. Rarity picked it up with her light blue magic.

"Quick! Now!" the Doctor yelled. Rarity quickly aimed the sonic at the Queen's horn and pressed down on a button. It caused her horn to flicker, making the knife drop from her grip where it had been pressed against the Doctor's throat. Then the white unicorn pointed it at the Time Lord, and the ropes released their hold on him.

"No!" Chrysalis threw herself at the group. Before they could register what was happening, Rarity was on the floor, blood pooling around her head. Sweetie Belle screamed, running towards her sister. Apple Bloom and Scootaloo held her back from the action. Chrysalis smacked Twilight into the wall, a crunching sound heard as her head collided with the marble. The unicorn fell onto the floor, the back of her mane coated in the red substance.

"Luna! Get the Doctor!" Celestia ordered, turning to face the changeling. Luna gave a hard flap of her wings and started towards the Time Lord.

"I think not!" Chrysalis shouted. Her horn, returning to normal, fired a blast at the Princess of the Night. Luna, totally unprepared, was struck with the beam. She cried out and fell, spiraling down. She smashed into the marble, still.

"Luna!" Princess Celestia shouted. She looked upon her sister's still body with wide eyes. The lavender orbs then switched their focus to the Queen. "You'll regret that!" She started after the changeling, horn lit brightly.

"Rainbow Dash!" Applejack hissed. She jerked her head towards the sonic screwdriver, which was lying across the room. Rainbow Dash nodded and went to retrieve it while the earth pony tended to Twilight. The pegasus got the sonic and flew up to the Doctor.

"I don't think so!" came Chrysalis's voice from below. The Doctor was picked up, held in a shifting green aura, and taken away from Dash.

"I think so!" Celestia shouted. There was a scream as the Sun Princess burnt the changeling with her magic. The Doctor fell out of the air, and was grabbed by Rainbow Dash.

"Quick! Gimme the sonic!" the Time Lord demanded immediately.

"Alright, alright, here you go," Rainbow Dash said, hoofing it over. He grabbed it and aimed it at the changeling. The Queen's horn spluttered again, ending her magical flow. She hissed and was then hit with a barrage of blows from Celestia, the power of the sun on her side. The regal alicorn sprang forward, tackling Chrysalis into the floor.

"Okay, what now? Your plan worked- somewhat, anyways," Dash commented. She hovered with the Time Lord in her arms.

"I, um, I don't know. I didn't think we'd get this far, actually," he replied.

"You're kidding me, right?" She gave him a deadpan stare.

The Doctor thought. "I think I know what to do. We'll need to get Luna up first." He pointed at the Night Princess, still lying unconscious on the floor. On wing was bent at an awkward angle, and blood was in a puddle around her.

A high pitched scream went through the room. Celestia was frozen, her body still. She looked like she had been turned to stone, but still retained her color. The Princess's face was stuck in a look of horror and pain. Chrysalis smirked, laughing.

"Hello Dissy! Wanna play?" the Queen giggled evilly, advancing towards the draconequus. Discord grimaced, backing away.

"No, not really, I'm kinda tired, actually," Discord grunted. He put up his paws in defeat.

"But I want to, and that's all that matters!" She pounced on the spirit, who promptly teleported out of the way. He waved, panicked, at her from the ceiling. Chrysalis blasted him from below, and pounced on top of him, sitting on his chest. She bent down and whispered something in his ear. "I think I'm going to have fun with you."

Rainbow Dash grimaced, ears folding back. "Doctor! We need to do something!"

"I'm thinking, I'm thinking!" he replied frantically, pulling at his hair. Rainbow stared as he did this, eyes wide. His hair was great.

His head popped up, face bright. "I know!" He got his sonic screwdriver and pointed it at not Chrysalis, but _Discord_, and pressed down.

The Lord of Chaos exploded with golden magic, throwing the Queen off and into a wall. Discord was lifted into the air, his magic going crazy. It went for Chrysalis and attacked her itself, not taking any command from Discord, who was pretty confused.

"What's happening?" Dash asked, eyebrows raised as she watched Chrysalis scream as she was hit repeatedly. After the Queen was unconscious, the golden tendrils spread across Equestria, paralyzing all the changelings. Discord flashed once more with another burst of magic, and every single changeling was turned to dust, even Chrysalis. After it all, the spirit fell out of the air. He landed on the ground and didn't wake up.

"What."

Rainbow Dash stared in awe at the place where Chrysalis had once been. Just a small pile of ashes.

"Well, that turned out better than expected. Well, not really, well, I don't know. Come on, to the ground! There are some injured ponies we need to take care of," the Doctor said. Rainbow Dash flew them both down. Her heart was pounding wildly, and it wasn't because of what she had just witnessed. He just saved Equestria and defeated the Queen. He had known to sonic Discord, causing his magic to react. Rainbow loved danger, and everything about it, even if she did get hurt. But even though he was an alien species, how could she not love how dangerous and smart he was? Even if he was an even bigger egghead than Twilight. There was no denying it now. Dash knew what the feeling was.

She was in love.


	9. We Won

The Doctor crouched next to Rarity, cleaning the blood off her wound. Her usually beautiful white coat was stained a deep red. Her head was cracked open from her horn to her ear. It was going to be hard to stop the bleeding with as large as the gash was, but they didn't have many choices. It was so bad they could see the skull clearly when the blood was cleaned off. If they did happen to find a hospital that was open, it would probably be packed.

Twilight's was not nearly as bad. She hit her head pretty hard, but the gash wasn't as bad. She definitely had a concussion, and Rarity too.

Luna had a broken wing, obviously, and some fur was burnt, but that was the extent of her injuries. Celestia was fine, except for a few bruises and burns also. Discord was still unconscious, along with Rarity and Twilight. Everypony else was okay, though the Doctor had a small cut on his throat from Chrysalis putting the blade of the knife up to it.

"Is Rarity going to be okay?" Sweetie Belle asked, her green eyes big and watery. She stared up at the Doctor, who was busy wrapping bandages around the unicorn's bloody head. He glanced down at her, unsure of what to say. Rarity's injury was fairly severe, and she had lost a lot of blood.

Deciding it was best to lie, instead of telling the filly that her sister might not be okay, he said, "Yeah, she'll be fine. No need to worry." Sweetie nodded without another sound and sat down, wrapping her tail around herself. She watched in silence as the Time Lord finished with Rarity for now and moved on to Twilight.

"How's she doing, Applejack?" the Doctor asked, kneeling down next to the orange earth pony. AJ grunted, pouring some alcohol on a small fabric pad and pressing it to the unicorn's purple head.

"Okay. Not the worst injury of us, that's for sure," she replied, glancing up at Rarity from across the room. Her emerald eyes teared up for a second, but quickly hardened. "Rarity . . . she could die, can't she?" Applejack looked up into the Doctor's brown eyes, studying them.

The Time Lord returned her gaze for as long as he could. The burning emerald gaze was soon too much for him, and he looked down at Twilight. ". . Yeah."

Applejack grunted again. "You better hope that doesn't happen." Ending with that semi-threatening note, the earth pony stood up and walked away, going to Apple Bloom. The Doctor didn't watch her leave; he just sat there, looking down at the pool of blood around Twilight's head.

Rainbow Dash hovered in the air, watching Fluttershy tend to Discord. She was busy snuggling him, and the blue pegasus was sure that if the spirit was awake right then, he would've gagged and turned her into butter. Snorting and rolling her eyes as her yellow feathered pal started singing her favorite lullaby to the unconscious draconequus, she turned her head. She was immediately met with the sight of the Doctor leaning against the wall, hands in his pockets; all alone. She glanced once more down at Fluttershy. She was curled next to Discord, her wing stroking his back. Rainbow decided that she definitely didn't want to stay, neither did she think that Fluttershy needed her help with anything. The pegasus gagged when she saw the other kiss Discord's face and flew away.

Rainbow Dash fluttered quietly over to the Doctor, spreading her wings to slow herself. She landed and closed her wings. "You look kinda lonely. Want some company?" she asked, smiling. Cerise eyes looked upwards at the six foot Time Lord. Her head felt fuzzy.

_Thump. Thump. Thump. _

The Doctor looked down and smiled. He slid down the wall until reaching her level. He plopped onto the ground and Dash did the same.

"If I looked lonely, it's because it's true," he responded halfheartedly. He smiled slightly but it disappeared.

"What's the matter?" Rainbow Dash asked, tilting her head. The Doctor ran a hand through his hair.

_Oh Celestia that's hot. _

"Well, it's all my fault. Rarity is injured, and she . . . she might die. Because of me. I _hate _it when people- or ponies, even- die because of me. This blood on my hands, no matter how hard I wash; even if I cut them off, or I regenerate, it will always be there. It just gets . . . tiring, sometimes, I guess," the Time Lord answered. Dash patted his back with a hoof.

"Come on, I'm sure she won't die. Rarity may be lady-like, but she's tough. She'll pull through." Rainbow gave him a smile. He glanced up at her from where he had his head in his hands.

"I hope you're right. I think Applejack will flay me if she does." Rainbow laughed, knowing full well she would also if Rarity did.

"Applejack wouldn't be alone," Dash joked, poking him in the ribs with her elbow. The Doctor joined in on the laughter.

"I think I'd be dead before I got through everyone who would," the Time Lord added. Rainbow fell over, holding her stomach.

"It's so true it's not even funny!"

"Then why are you laughing?"

Dash stopped momentarily. "I don't know!" They both erupted in laughter again. After a few more minutes of laughter, they were both done. The cyan pegasus sat up and wiped a tear from her eye, giving a content, shuddering sigh.

"I haven't laughed like that in a while," came the sudden voice from beside her.

The words came out of her mouth before she knew what she was doing. "If you let me come with you, I could make you laugh even more." She slapped a hoof over her mouth at what she just said, her cheeks turning red. Rainbow shrank down, hoping the floor would swallow her up. The Doctor looked at her, stunned. "Uhhh . . . oops?"

"You _want_ to come with me?" the Time Lord asked tentatively after several awkward filled minutes had passed.

Rainbow Dash whimpered slightly. "I-I'm sorry, I didn't mean to say that," she stammered, one hoof halfway covering her mouth, "it just came out! I-I. . ." She glanced away, tears ready to fall from her eyes as she squinted them shut. Then, she opened them.

Now was her chance. She could do this. She _would _do this.

Rainbow Dash stood up defiantly, turning to face the Doctor. "Y-yes! You know what, I did mean to say that! I _do _want to come with you! More than anything, in fact!" she said with confidence. "It's been a great adventure, with lots of danger, and I like that! I love danger!" She felt like exploding, seeing the shocked expression on the Doctor's face, but she kept her cool and continued. "And there's one thing I want even more." She gazed intently into the big brown eyes on front of her. "You." She leaned forward, pressing her lips against the Time Lord's. He jumped a little at first, but stayed in the kiss. Dash pushed more into it, her eyes closed. After another thirty seconds had passed, she pulled back. Her heart pounded so loud she was sure that everypony in the room could hear it, and her head spun. She glanced around, seeing all eyes on them. Rainbow froze, her face bright red. The Doctor's mouth was hanging open, eyes wide.

An awkward silence fell upon the room. Nopony spoke, or moved. Only astonished blinking. It was not for about another minute when a single clap of hooves echoed throughout the room. Everypony looked to Pinkie Pie, who had one hoof raised to hit the ground. She let it land, and another. The slow clap was a party of one, until Sweetie Belle joined in. The other Crusaders joined in after her.

Applejack locked eyes with the embarrassed pegasus. She nodded, and started clapping as well. The recently woken Night Princess was the next to join it, soon followed by Celestia. Fluttershy gave a quiet but determined "yay," sitting on her back legs to clap her front hooves together.

"Woo! Woo! Another!" Pinkie Pie started yelling, her clapping speed increasing tenfold. She bounced around, but stopped in midair as she saw the odd looks she was getting. She floated to the floor, smiling sheepishly. She raised a hoof in front of her. "Eh he, woo . . .?"

"I am incredibly confused," the Doctor stated.

"Ah'm gonna flay him," Applejack deadpanned.

"I agree with Applejack! We're going to flambé you!" Pinkie Pie shouted. Every head slowly turned to look at her. "What?" She sighed. "Doctor, she just announced-" Pinkie leaned backwards, tottering on one back leg, front hooves clasped together "-_love._" The party pony finished a complete circle, walking upside down and coming back down in the right direction. "And you're _confused_?! Are you _kidding _me right now?! Even I'm not _that _oblivious!" she scoffed, shaking her head disapprovingly.

"Doctor, the truth is," Rainbow Dash began, closing her eyes, "I may have hated you in the beginning; because, you know, almost killed me with your TARDIS." She paused, waving a blue hoof. "After all we went through, though, I got to know you. You like danger, and we're constantly running, which I think is great. And, if it's okay, I'd like to go with you on your adventures." She smiled at the Time Lord.

"Well, Dash, I think that'd be fine," the Doctor said, returning the smile. "But only if it's okay with your pals first." He looked over at the watching ponies.

"Fine with me! Just get me a souvenir or two while you're out and about!" Pinkie chimed. She gasped suddenly. "And don't forget to come back for birthdays! I have some great parties planned out this year!"

"Ah don't know," Applejack started, rubbing the back of her head with a hoof, "it's a might dangerous. But if it's what you want, then go for it." She grinned. "Make sure we can get in contact with ya, though, in case we need to fight some evil with the Elements of Harmony." AJ winked.

Fluttershy smiled. "I hope you're happy with it."

Rainbow Dash rolled her eyes. "Jeez, it's not like we're leaving now!"

* * *

Luckily, there was a hospital open in Ponyville that had survived most of the attack. Rarity was going to be fine, and so were the others. Although, one would not make the safe zone just quite yet. Discord was in a coma, thanks to the excessive amount of magic pouring out of him at the same time. But the nurses said he would wake up within the week, when his magic returned.

But thirty-two staples later, and some puking, Rarity was already awake and on the road to recovery. They were all surprised to hear of Rainbow Dash's confession of her feelings, and that she wanted to leave. Twilight was skeptical at first, but after some prompting from Rarity, she begrudgingly agreed. The Doctor gave Twilight a cellphone, one that could call anywhere in space and time. When she had been handed it, the first words to come out of her mouth were:

"Dafuq?"

Upon arriving at the library, Twilight also reunited with Spike, who had become trapped in the basement when he hid from the changelings. He was completely fine, if not a little dirty and hungry.

So the ponies mourned their lost loved ones, and repaired the damages caused by the changelings. After a few days, the Doctor grew agitated by not finding the TARDIS. (It had ended up rematerializing in Saddle Arabia). The Time Lord decided they were going to be off. He would not wait a moment longer.

As the Doctor made a few little repairs to the TARDIS, Rainbow Dash chatted with her friends. They sat around a small table outside of a restaurant.

"So, big day, huh?" Rarity asked, sipping daintily at her iced tea. She was wearing her sunglasses, with her hair tied into a ponytail, and her yellow headband with gems on it. It partially covered her bandages, which was only part of the reason she wore the item. She was also regaining the use of her magic, as her horn had been damaged by the accident. It still spazzed occasionally, but not too bad.

Rainbow Dash ate a hay fry. "Yeah. I can't wait. I wonder where we'll end up." She gazed into the distance, eyes sparkling.

"Hey, Dash, can Ah ask you somethin'?" Applejack questioned. She tipped her hat back slightly on her head.

"Sure, AJ. Fire away." She perked an ear.

"If you're Loyalty, then how come you're leavin'?"

Rainbow smirked. "That's easy. But you girls do know I will miss you, right? With all my heart?" They all nodded. "Well, AJ, the answer is I've found someone else to be loyal to."

"Rainbow Dash! TARDIS is ready!" the Doctor called from the spacecraft. The ponies looked over at the blue box, which was sitting, eager to be off again.

Dash smiled, tears in her eyes. "Bye girls!" They all went in for a group hug, and Pinkie Pie took out her camera quickly. She held it above them, her arm stretching to super-pony lengths, and snapped a photo. Flashing another glance at them as she raced towards the TARDIS, Rainbow Dash grinned. She got five hoof waves back. She kissed her hoof and waved at them, flitting into the air slightly, and disappeared inside the TARDIS. The last thing she heard was crying, and Pinkie Pie yelling:

"Oh my Dashie is all grown up!"

The Doctor turned to Dash, a grin on his face. "You ready?" He was leaning over the control center.

Rainbow Dash returned the grin. "Oh yeah!" The Time Lord pulled a lever, and they were off. The sound of the engines, plus the Doctor leaving the brakes on, filled her ears. It was when she started feeling sick that Dash looked at her hooves, trying to get her mind off the nausea.

Rainbow Dash screamed as her body started changing.

* * *

_**That's it for now. Not the end of the series though! Look out for sequels and mini stories!**_

_**Randomest hamster out yo. **_


End file.
